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<!DOCTYPE html>
<html lang="en">
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  <head>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1">
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    <title>Jflow</title>

    <!-- Bootstrap core CSS -->
    <link href="css/bootstrap.min.css" rel="stylesheet">
    <!-- Bootstrap theme -->
    <link href="css/bootstrap-theme.min.css" rel="stylesheet">

    <!-- Custom styles for this template -->
    <link href="css/theme.css" rel="stylesheet">
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	<!--  Highlight code -->
	<link href="css/tomorrow-night-eighties.css" rel="stylesheet">
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    <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
    <!--[if lt IE 9]>
      <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
    <![endif]-->
  </head>
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  <body role="document">
  
    <!-- Fixed navbar -->
    <div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
      <div class="container">
        <div class="navbar-header">
          <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
            <span class="sr-only">Toggle navigation</span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
          </button>
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          <a class="navbar-brand" href="./index.html">Jflow</a>
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        </div>
        <div class="navbar-collapse collapse">
          <ul class="nav navbar-nav">
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            <li><a href="./index.html">About</a></li>
            <li><a href="./jflow_install.html">Install</a></li>
            <li><a href="./jflow_quickstart.html">Quick start</a></li>
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            <li class="dropdown active">
              <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
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              <ul class="dropdown-menu" role="menu">
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                <li class="active"><a href="./jflow_core_workflow.html">Add a workflow</a></li>
                <li><a href="./jflow_core_component.html">Add a component</a></li>
                <li><a href="./jflow_plugin.html">Plugin insertion</a></li>
                <li><a href="./jflow_type.html">Add a data type</a></li>
                <li><a href="./jflow_format.html">Add a file format</a></li>
                <li><a href="./jflow_advanced_configuration.html">Advanced configuration</a></li>
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              </ul>
            </li>
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			<li><a href="./example1.html">Example</a></li>
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			<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
          </ul>
        </div><!--/.nav-collapse -->
      </div>
    </div>
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    <div class="container">
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      <div class="row">
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        <!--Nav Bar -->
	    <nav class="col-xs-3 bs-docs-sidebar">
	        <ul id="sidebar" class="nav nav-stacked fixed">
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		        <li><a href="#what" class="active">What is a workflow</a></li>
		        <li><a href="#workflow-architecture">Where to add a new workflow</a></li>
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		        <li><a href="#workflow" >The Workflow class</a></li>
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		       	<li><a href="#define_parameters">Define parameters</a>
			       	<ul class="nav nav-stacked">
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			       		<li><a href="#parameters">Parameters</a></li>
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			       		<li><a href="#input_parameters">Inputs</a></li>
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			       		<li><a href="#multiple_parameters">Multiple parameters</a></li>
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			       		<li><a href="#exclusion_rules">Exclusion rules</a></li>
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	                </ul>
                </li>
				<li><a href="#process">Process</a></li>
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				<li><a href="#other_methods">Other methods</a>
				  	<ul class="nav nav-stacked">
				        <li><a href="#pre_process">Pre process</a></li>
						<li><a href="#post_process">Post process</a></li>
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						<li><a href="#set_to_address">Set to address</a></li>
						<li><a href="#set_subject">Set subject</a></li>
						<li><a href="#set_message">Set message</a></li>
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						<li><a href="#get_resource">Get resource</a></li>
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					</ul>
				</li>
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				<li><a href="#your-rules">Custom rules</a>
					<ul class="nav nav-stacked">
						<li><a href="#simple-rules">Simple rules</a></li>
						<li><a href="#link-rules">Link rules</a></li>
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                        <li><a href="#conditional-rules">Conditional rules</a></li>
						<li><a href="#raise-error-warning">Raise an error or a warning in a rule</a></li>
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					</ul>
				</li>
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	        </ul>
   	    </nav>
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        <div class="col-xs-12 col-sm-9">
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           	<section id="what" class="group">
		    	<h1 class="page-header">What is a workflow</h1>
	    		<p>A workflow is a collection of <a href="./jflow-core-component.html">components</a>. In jflow, it is represented by a Python class
	    			inerhiting from <code>jflow.workflow.Workflow</code>. It lists all the inputs and parameters that should be requested to 
	    			the final user and build the execution process by adding components and linking them to each others.</p>
	    	</section>
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        	<section id="workflow-architecture" class="group">
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		    	<h1 class="page-header">Where to add a new workflow</h1>
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		    	<p>New wokflow must be added as a new python package in the <code>workflows</code> package. The implementation of
		    	a workflows must be written in the package <code>__init__.py</code> file. The developper can also create: </p>
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		    	<ul>
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		    		<li>a <code>components</code> package, where all the workflow specific components can be stored,</li>
		    		<li>a <code>lib</code> package to import specific libraries within its workflow,</li>
		    		<li>a <code>bin</code> folder with the binaries used in the workflow.</li>
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		    	</ul>
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		    	<pre class="pre-hl "><code class="ini">jflow/
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├── bin/
├── docs/
├── src/
├── workflows/
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│   ├── myworkflow/       [ the new workflow package ]
│   │   ├── components/   [ specific components ]
│   │   ├── lib/          [ specific libraries ]
│   │   ├── bin/          [ specific binairies ]
│   │   └── __init__.py   [ the workflow implementation ]
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│   ├── components/
│   ├── extparsers/
│   ├── __init__.py
│   ├── formats.py
│   └── types.py
├── applications.properties
└── README</code></pre>
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		    </section>
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        	<section id="workflow" class="group">
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		    	<h1 class="page-header">The Workflow class</h1>
		    	<p>In jflow, a workflow is a class defined in the <code>__init__.py</code> file. In order to add a new workflow, the developper has to: </p>
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		    	<ul>
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			    	<li>implement a class inheriting from the <code>jflow.workflow.Workflow</code> class,</li>
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					<li>overload the <code>get_description()</code> method to provide to the final user a description of the workflow,</li>
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					<li>overload the <code>define_parameters()</code> method to add the workflow inputs and parameters,</li>
					<li>overload the <code>process()</code> method by adding components and setting their arguments,</li>
					<li>link the components inputs and outputs.</li>
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				</ul>
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				<p>The class skeleton is given by</p>
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			    <div>
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			    	<pre class="pre-hl "><code class="python">from jflow.workflow import Workflow
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class MyWorkflow (Workflow):
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    def get_description(self):
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        return "a description"
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    def define_parameters(self, function="process"):
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        # define the parameters
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    def process(self):
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        # add and link the components</code></pre>
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			    </div>
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			</section>
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			<section id="define_parameters" class="group">
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		    	<h1 class="page-header">Define parameters</h1>
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				<p>
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					The <code>define_parameters()</code> method is used to add workflow parameters and inputs. To do so, several methods are available.
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					Once defined, the new parameters are available as object attibuts, thus they are accessible through <code>self.parameter_name</code>.
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				</p>
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				<p>
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					Several types of parameters can be added, all described in the following sections. All have two required positional
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					arguments: <code>name</code> and <code>help</code>. The other arguments are optional and can be given to the method by using their 
					keywords.
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				</p>
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				<div class="alert alert-info" role="alert">
					<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
					The operator <code>is</code> is not supported to evaluate a parameter, the operator <code>==</code> must be prefered.
				</div>
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				<div id="parameters" class="subgroup">
					<h2>Parameters</h2>
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					<p>Parameters can be added to handle a single element or a list of elements. Thus, the <code>add_parameter()</code> method can be used to force
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					the final user to provide one and only one value, where the <code>add_parameter_list()</code> method allows the final user to give as many values he 
					wants.</p>
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					<h3>add_parameter()</h3>
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						<h4>Example</h4>
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						<p>
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							In the following example, a parameter named <code>sequencer</code>
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							is added to the workflow. It has a list of choices and the default value is "HiSeq2000".
						</p>
				    	<div>
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				    		<pre class="pre-hl "><code class="python">self.add_parameter("sequencer",
    		   "The sequencer type.", 
    		   choices = ["HiSeq2000", "ILLUMINA","SLX","SOLEXA","454","UNKNOWN"], 
    		   default="HiSeq2000")</code></pre>
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				    	</div>
						
						<h4>Options</h4>
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			    			<p>There are two positional arguments: <code>name</code> and <code>help</code>. All other options are keyword options</p>
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							<div class="table-responsive">
								<table class="table table-bordered table-striped">
									<thead>
										<tr>
											<th>Name</th>
											<th>Type</th>
											<th>Required</th>
											<th>Default value</th>
											<th>Description</th>
										</tr>
									</thead>
									<tbody>
										<tr>
											<td>name</td>
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											<td>string</td>
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											<td>true</td>
											<td>None</td>
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											<td>The name of the parameter. The parameter value is accessible 
												within the workflow object through the attribute named <code>self.parameter_name</code>.</td>
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										</tr>
										
										<tr>
											<td>help</td>
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											<td>string</td>
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											<td>true</td>
											<td>None</td>
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											<td>The parameter help message.</td>
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										</tr>
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										<tr>
											<td>default</td>
											<td>-</td>
											<td>false</td>
											<td>None</td>
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											<td>The default parameter value. It's type depends on the parameter type.</td>
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										</tr>
										
										<tr>
											<td>type</td>
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											<td>string</td>
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											<td>false</td>
											<td>"str"</td>
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											<td>The parameter type. The value provided by the final user will be casted and checked against this type. 
											All built-in Python types are available "int", "str", "float", "bool", "date", ... To create customized types, 
											refere to the <a href="./jflow-type.html">Add a data type</a> documentation.</td>
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										</tr>
										
										<tr>
											<td>choices</td>
											<td>list</td>
											<td>false</td>
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											<td>[]</td>
											<td>A list of the allowed values.</td>
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										</tr>
										
										<tr>
											<td>required</td>
											<td>boolean</td>
											<td>false</td>
											<td>false</td>
											<td>Wether or not the parameter can be ommitted.</td>
										</tr>
										
										<tr>
											<td>flag</td>
											<td>string</td>
											<td>false</td>
											<td>None</td>
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											<td>The command line flag (if the value is None, the flag will be <code>--name</code>).</td>
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										</tr>
										
										<tr>
											<td>group</td>
											<td>string</td>
											<td>false</td>
											<td>"default"</td>
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											<td>The value is used to group a list of parameters in sections. The group is used in both command line and GUI.</td>
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										</tr>
										
										<tr>
											<td>display_name</td>
											<td>string</td>
											<td>false</td>
											<td>None</td>
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											<td>The parameter name that should be displayed on the final form.</td>
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										</tr>
										
										<tr>
											<td>add_to</td>
											<td>string</td>
											<td>false</td>
											<td>None</td>
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											<td>If this parameter is part of a multiple parameter, <code>add_to</code> allows to define to which "parent" parameter it should be
											linked to.</td>
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										</tr>
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										<tr>
											<td>rules</td>
											<td>string</td>
											<td>false</td>
											<td>None</td>
											<td>Define custom rules on the parameter. Rules are separated by a ";"<br/>
												Available rules:<br/>
												<ul>
													<li><strong>Exclude:</strong> exclude parameters. If one is given, the other must be not given.<br/>
													<em>Syntax: Exclude=param1,param2,...</em></li>
													<li><strong>ToBeRequired:</strong> require other parameters if parameter is given.<br/>
													<em>Syntax: ToBeRequired=param1,param2,...</em></li>
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													<li><strong>RequiredIf:</strong> parameter is required only if other parameters have (or have not) some values.<br/>
													<em>Syntax: RequiredIf?(ANY|ALL)[param_1=value1,param_2!=value2,...] (all conditions or any condition)</em><br/>
														Special values: * for any value of the parameter (not empty), None for not given (or empty)<br/>
													Example: RequiredIf?ANY[adapter_1!="AATGC",adapter_2=*,gtf_file=None]</li>
													<li><strong>ActivateIf:</strong> parameter is enabled only if other parameters have some values.<br/>
													<em>Syntax (like RequiredIf rule):<br/></br:>ActivateIf?(ANY|ALL)[param_1=value1,param_2=value2,...]</em> (all conditions or any condition)</li>
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												</ul>
											</td>
										</tr>
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									</tbody>
								</table>
							</div>
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					<h3>add_parameter_list()</h3>
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						<p>The <code>add_parameter_list()</code> method takes the same arguments as <code>add_parameter()</code>. However, adding this parameter,
						the final user will be allowed to enter multiple values for this parameter and the object attribut <code>self.parameter_name</code> will be
						settled as a Python list.</p>
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				</div>
				
	       		
	       		<div id="input_parameters" class="subgroup">
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	       			<h2>Inputs</h2>
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					<p>Just like parameters, inputs can be added to handle a single file or a list of files. Thus, the <code>add__input_file()</code> method can be used to force
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					the final user to provide one and only one file, where the <code>add__input_file_list()</code> method allows the final user to give as many files as he
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					wants.</p>
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	       				<h3>add_input_file()</h3>
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							<h4>Example</h4>
	       				<p>
							In the following example, an input named <code>reads</code> 
							is added to the workflow. The provided file is required and should be in fastq format. No file size limitation is specified. 
						</p>
				    	<div>
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				    		<pre class="pre-hl "><code class="python">self.add_input_file_list("reads", 
                         "Which read files should be used", 
                         file_format="fastq", 
                         required=True)</code></pre>
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				    	</div>
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							<h4>Options</h4>
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								<p>There are two positional argument : <code>name</code> and <code>help</code>. All other options are keyword options. </p>
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								<div class="table-responsive">
									<table class="table table-bordered table-striped">
										<thead>
											<tr>
												<th>Name</th>
												<th>Type</th>
												<th>Required</th>
												<th>Default value</th>
												<th>Description</th>
											</tr>
										</thead>
										<tbody>
											<tr>
												<td>name</td>
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												<td>string</td>
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												<td>true</td>
												<td>None</td>
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												<td>The name of the parameter. The parameter value is accessible 
													within the workflow object through the attribute named <code>self.parameter_name</code>.</td>
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											</tr>
											
											<tr>
												<td>help</td>
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												<td>string</td>
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												<td>true</td>
												<td>None</td>
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												<td>The parameter help message.</td>
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											</tr>
											
											<tr>
												<td>default</td>
												<td>string</td>
												<td>false</td>
												<td>None</td>
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												<td>The default path value.</td>
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											</tr>
										
											<tr>
												<td>file_format</td>
												<td>string</td>
												<td>false</td>
												<td>"any"</td>
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												<td>The file format is checked before running the workflow. To create customized format, 
													refere to the <a href="./jflow-format.html">Add a file format</a> documentation.</td>
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											</tr>
											
											<tr>
												<td>type</td>
												<td>string</td>
												<td>false</td>
												<td>"inputfile"</td>
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												<td>The type can be "inputfile", "localfile", "urlfile" or "browsefile". An "inputfile" allows the 
												final user to provide a "localfile" or an "urlfile" or a "browsefile". A "localfile" restricts the final
												user to provide a path to a file visible by jflow. An "urlfile" only permits the final user to give an 
												URL as input, where a "browsefile" force the final user to upload a file from its own computer. This last
												option is only available from the GUI and is considered as a "localfile" from the command line. All the 
												uploading process is handled by jflow.</td>
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											</tr>
											
											<tr>
												<td>required</td>
												<td>boolean</td>
												<td>false</td>
												<td>false</td>
												<td>Wether or not the parameter can be ommitted.</td>
											</tr>
											
											<tr>
												<td>flag</td>
												<td>string</td>
												<td>false</td>
												<td>None</td>
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												<td>The command line flag (if the value is None, the flag will be <code>--name</code>).</td>
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											</tr>
											
											<tr>
												<td>group</td>
												<td>string</td>
												<td>false</td>
												<td>"default"</td>
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												<td>The value is used to group a list of parameters in sections. The group is used in both command line and GUI.</td>
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											</tr>
											
											<tr>
												<td>display_name</td>
												<td>string</td>
												<td>false</td>
												<td>None</td>
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												<td>The parameter name that should be displayed on the final form.</td>
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											</tr>
											
											<tr>
												<td>add_to</td>
												<td>string</td>
												<td>false</td>
												<td>None</td>
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												<td>If this parameter is part of a multiple parameter, <code>add_to</code> allows to define to which "parent" parameter it should be
												linked to.</td>
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											</tr>
											
											<tr>
												<td>size_limit</td>
												<td>string</td>
												<td>false</td>
												<td>"0"</td>
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												<td>Which maximum file size is allowed. If the value is "0", the file size allowed is unlimited. The given value should
												also provides the file size units between "bytes", "Kb", "Mb", "Gb", "Tb", "Pb", "Eb" and "Zb". A value of 10Mb will 
												restrict the user to upload a file of 10 Mega Bytes.</td>
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											</tr>
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											<tr>
												<td>rules</td>
												<td>string</td>
												<td>false</td>
												<td>None</td>
												<td>Define custom rules on the parameter. Rules are separated by a ";"<br/>
													Available rules:<br/>
													<ul>
														<li><strong>Exclude:</strong> exclude parameters. If one is given, the other must be not given.<br/>
														<em>Syntax: Exclude=param1,param2,...</em></li>
														<li><strong>ToBeRequired:</strong> require other parameters if parameter is given.<br/>
														<em>Syntax: ToBeRequired=param1,param2,...</em></li>
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														<li><strong>RequiredIf:</strong> parameter is required only if other parameters have (or have not) some values.<br/>
														<em>Syntax: RequiredIf?(ANY|ALL)[param_1=value1,param_2!=value2,...] (all conditions or any condition)</em><br/>
														Special values: * for any value of the parameter (not empty), None for not given (or empty)<br/>
														Example: RequiredIf?ANY[adapter_1!="AATGC",adapter_2=*,gtf_file=None]</li>
														<li><strong>ActivateIf:</strong> parameter is enabled only if other parameters have some values.<br/>
														<em>Syntax (like RequiredIf rule):<br/></br:>ActivateIf?(ANY|ALL)[param_1=value1,param_2=value2,...]</em> (all conditions or any condition)</li>
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														<li><strong>UniqueAll:</strong> the file given for this parameter must be not given for another one</li>
														<em>Syntax: Unique</em>
														</ul>
												</td>
											</tr>
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										</tbody>
									</table>
								</div>
								
					    <h3>add_input_file_list()</h3>
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						<p>This method takes the same arguments as <code>add_input_file()</code>. However, adding this parameter,
						the final user will be allowed to provide multiple files and the object attribut <code>self.parameter_name</code> will be
						settled as a Python list.</p>
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						<p>The <code>rules</code> argument has a rule available only on input files list: Unique. If this rule is given, a same file must be unique on the list.</p>
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						<h3>add_input_directory()</h3>
						<p>
							The <code>add_input_directory()</code> method allows the user to select files from a specific directory. This 
							kind of input can be useful for tools outputing not only files but an organized directory.
							The parameter <code>get_files_fn</code> specify the function that will be used to retrieve the files. This method can 
							take as many arguments as required, but the first argument has to be a string representing the folder path.
							By default all files will be selected. From the workflow <code>process()</code> function, the files can be retrieved
							by using the <code>get_files()</code> method.
						</p>
						
						<h4>Example</h4>
	       				<p>
	       					In the following example, the <code>add_input_directory()</code> method is used to parse a directory and retrieve only fasta files
	       					inside this directory. <code>get_files()</code> will browse the directory and get all fasta files.
						</p>
			    		<div>
			    		<pre class="pre-hl "><code class="python">import os
from jflow.Workflow import Workflow

def fasta_files(folder):
    res = []
    for file in os.listdir(folder):
        if file.endswith(".fasta"):
            res.append(file)
    return res

class MyWorkflow(Workflow):
    def define_parameters(self, function="process"):
        self.add_input_directory("fastadir", "Path to folder with fasta files", 
            get_files_fn=fasta_files)

    def process(self):
        # to retrieve the files
        for fastafile in self.fastadir.get_files():
            # do something</code></pre>
				    	</div>
				    		
			    		<h4>Options</h4>
						<p>There are two positional argument : <code>name</code> and <code>help</code>. All other options are keyword options. </p>
						<div class="table-responsive">
							<table class="table table-bordered table-striped">
								<thead>
									<tr>
										<th>Name</th>
										<th>Type</th>
										<th>Required</th>
										<th>Default value</th>
										<th>Description</th>
									</tr>
								</thead>
								<tbody>
									<tr>
										<td>name</td>
										<td>string</td>
										<td>true</td>
										<td>None</td>
										<td>The name of the parameter. The parameter value is accessible 
											within the workflow object through the attribute named <code>self.parameter_name</code>.</td>
									</tr>
									
									<tr>
										<td>help</td>
										<td>string</td>
										<td>true</td>
										<td>None</td>
										<td>The parameter help message.</td>
									</tr>
									
									<tr>
										<td>default</td>
										<td>string</td>
										<td>false</td>
										<td>None</td>
										<td>The default path value.</td>
									</tr>
								
									<tr>
										<td>get_files_fn</td>
										<td>function</td>
										<td>false</td>
										<td>-</td>
										<td>
											get_files_fn will be the method called when executing <code>param.get_files()</code>. All argument from get_files()
											will be used as arguments in get_files_fn
										</td>								
									</tr>
									
									<tr>
										<td>required</td>
										<td>boolean</td>
										<td>false</td>
										<td>false</td>
										<td>Wether or not the parameter can be ommitted.</td>
									</tr>
									
									<tr>
										<td>flag</td>
										<td>string</td>
										<td>false</td>
										<td>None</td>
										<td>The command line flag (if the value is None, the flag will be <code>--name</code>).</td>
									</tr>
									
									<tr>
										<td>group</td>
										<td>string</td>
										<td>false</td>
										<td>"default"</td>
										<td>The value is used to group a list of parameters in sections. The group is used in both command line and GUI.</td>
									</tr>
									
									<tr>
										<td>display_name</td>
										<td>string</td>
										<td>false</td>
										<td>None</td>
										<td>The parameter name that should be displayed on the final form.</td>
									</tr>
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								<tr>
									<td>rules</td>
									<td>string</td>
									<td>false</td>
									<td>None</td>
									<td>Define custom rules on the parameter. Rules are separated by a ";"<br/>
										Available rules:<br/>
										<ul>
											<li><strong>Exclude:</strong> exclude parameters. If one is given, the other must be not given.<br/>
											<em>Syntax: Exclude=param1,param2,...</em></li>
											<li><strong>ToBeRequired:</strong> require other parameters if parameter is given.<br/>
											<em>Syntax: ToBeRequired=param1,param2,...</em></li>
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											<li><strong>RequiredIf:</strong> parameter is required only if other parameters have (or have not) some values.<br/>
												<em>Syntax: RequiredIf?(ANY|ALL)[param_1=value1,param_2!=value2,...] (all conditions or any condition)</em><br/>
												Special values: * for any value of the parameter (not empty), None for not given (or empty)<br/>
												Example: RequiredIf?ANY[adapter_1!="AATGC",adapter_2=*,gtf_file=None]</li>
											<li><strong>ActivateIf:</strong> parameter is enabled only if other parameters have some values.<br/>
													<em>Syntax (like RequiredIf rule):<br/></br:>ActivateIf?(ANY|ALL)[param_1=value1,param_2=value2,...]</em> (all conditions or any condition)</li>
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										</ul>
									</td>
								</tr>
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								</tbody>
							</table>
						</div>
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	       		</div>
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				<div id="multiple_parameters" class="subgroup">
					<h2>Multiple parameters</h2>
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						<p>Jflow offers, to the developper, the possibility to structure the input data by using the notion of multiple parameters. A multi 
						parameter is a collection of parameters linked together. Just like for parameters and inputs, it can be added to handle a single collection or a 
						list of collections. Thus, the <code>add_multiple_parameter()</code> method can be used to force the final user to provide one and only one 
						collection, where the <code>add_multiple_parameter_list()</code> method allows the final user to give as many collection he wants. To add a 
						parameter within the multiple parameter, it only requires to set the option <code>add_to</code> of any methods previously described. 
						The accessible object attribut <code>self.multi_parameter_name</code> is then a Python dictionary gathering all the values of the different 
						parameters under the format <code>{"sub_parameter1":value}</code></p>
						
						<h3>add_multiple_parameter()</h3>
						
						<h4>Example</h4>
						The following example creates a multiple parameter named <code>library</code> which contains two input files <code>R1</code> and <code>R2</code> 
						and a <code>sequencer</code> parameter. </p>
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				    	<div>
				    		<pre class="pre-hl "><code class="python">self.add_multiple_parameter("library", "Library.", required=True)
self.add_input_file("R1", "Path to R1 file.", required=True, add_to="library")
self.add_input_file("R2", "Path to R2 file.", add_to="library")
self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
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    "ILLUMINA", "UNKNOWN"], default="HiSeq2000", add_to="library")</code></pre>
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				    	</div>
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						<h4>Options</h4>
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						<p>There are two positional arguments : name and help. All other options are keyword options.</p>
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								<div class="table-responsive">
										<table class="table table-bordered table-striped">
											<thead>
												<tr>
													<th>Name</th>
													<th>Type</th>
													<th>Required</th>
													<th>Default value</th>
													<th>Description</th>
												</tr>
											</thead>
											<tbody>
												<tr>
													<td>name</td>
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													<td>string</td>
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													<td>true</td>
													<td>None</td>
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													<td>The name of the multi parameter. The parameter value is accessible 
														within the workflow object through the attribute named <code>self.multi_parameter_name</code>. And its sub parameters
														using <code>self.multi_parameter_name["sub_parameter_name"]</code>.</td>
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												</tr>
												
												<tr>
													<td>help</td>
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													<td>string</td>
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													<td>true</td>
													<td>None</td>
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													<td>The parameter help message.</td>
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												</tr>

												<tr>
													<td>required</td>
													<td>boolean</td>
													<td>false</td>
													<td>false</td>
													<td>Wether or not the parameter can be ommitted.</td>
												</tr>
												
												<tr>
													<td>flag</td>
													<td>string</td>
													<td>false</td>
													<td>None</td>
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													<td>The command line flag (if the value is None, the flag will be <code>--name</code>). The sub parameters can be set as following
													<code>--name sub1=... sub2=...</code></td>
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												</tr>
												
												<tr>
													<td>group</td>
													<td>string</td>
													<td>false</td>
													<td>"default"</td>
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													<td>The value is used to group a list of parameters in sections. The group is used in both command line and GUI.</td>
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												</tr>
												
												<tr>
													<td>display_name</td>
													<td>string</td>
													<td>false</td>
													<td>None</td>
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													<td>The parameter name that should be displayed on the final form.</td>
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												</tr>
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												<tr>
													<td>rules</td>
													<td>string</td>
													<td>false</td>
													<td>None</td>
													<td>Define custom rules on the parameter. Rules are separated by a ";"<br/>
														Available rules:<br/>
														<ul>
															<li><strong>Exclude:</strong> exclude parameters. If one is given, the other must be not given.<br/>
															<em>Syntax: Exclude=param1,param2,...</em></li>
															<li><strong>ToBeRequired:</strong> require other parameters if parameter is given.<br/>
															<em>Syntax: ToBeRequired=param1,param2,...</em></li>
														</ul>
													</td>
												</tr>
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											</tbody>
										</table>
									</div>
						
						<h3>add_multiple_parameter_list()</h3>
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						<p>This method takes the same arguments as <code>add_multiple_parameter()</code>. However, adding this parameter,
						the final user will be allowed to provide multiple collection and the object attribut <code>self.multi_parameter_name</code> will be
						settled as a Python list of Python dictionary.</p>
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				</div>
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			</section>
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	  		<section id="process" class="group">
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		    	<h1 class="page-header">Process</h1>
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		    	<p>The <code>process()</code> method is in charge of building the workflow by adding components (using the method <code>add_component()</code>) and
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		    	linking their inputs and their outputs. A component is a class representing a workflow step. See the
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		    	<a href="./jflow-core-component.html">component</a> documentation for more information.</p>
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   				<h2>add_component()</h2>
   				<p>The <code>add_component()</code> method add a component to the workflow by building a <code>jflow.component.Component</code>
   				object and returning it. All attributs defined within this object, such as the outputs, are then available from the workflow and 
   				can be used as inputs of other components.</p>
   				<h3>Example</h3>
   				<p>In the following example, the first component <code>BWAIndex</code> is built and returned in the <code>bwaindex</code> object.
   				The output <code>bwaindex.databank</code> is accessible as an object attribut and can be used as input of the <code>BWAmem</code>
   				component. This example is extracted from the <a href="./jflow-quickstart.html">Quick start</a>.</p>
					<div>
				    <pre class="pre-hl "><code class="python"># index the reference genome
bwaindex = self.add_component("BWAIndex", [self.reference_genome])
# align reads against the indexed genome
bwamem = self.add_component("BWAmem", [bwaindex.databank, self.reads])</code></pre>
				    	</div>
   				<h3>Options</h3>
   				<p>There is one positional argument : component_name. All other options are keyword options.</p>
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   				<div class="table-responsive">
					<table class="table table-bordered table-striped">
						<thead>
							<tr>
								<th>Name</th>
								<th>Type</th>
								<th>Required</th>
								<th>Default value</th>
								<th>Description</th>
							</tr>
						</thead>
						<tbody>
							<tr>
								<td>component_name</td>
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								<td>string</td>
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								<td>true</td>
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								<td>None</td>
								<td>The component class name to add to the workflow.</td>
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							</tr>
							<tr>
								<td>args</td>
								<td>list</td>
								<td>false</td>
								<td>[]</td>
								<td>The component's arguments (see <a href="./jflow-core-component.html#define_parameters">here</a> for more details).</td>
							</tr>
							<tr>
								<td>kwargs</td>
								<td>dict</td>
								<td>false</td>
								<td>{}</td>
								<td>The component's keyword arguments (see <a href="./jflow-core-component.html#define_parameters">here</a> for more details).</td>
							</tr>
							<tr>
								<td>component_prefix</td>
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								<td>string</td>
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								<td>false</td>
								<td>"default"</td>
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								<td>The prefix is used to name the component at the execution. The prefix allows to add multiple components of the same class within
								the same workflow.</td>
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							</tr>
						</tbody>
					</table>
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				</div>
			</section>
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	  		<section id="other_methods" class="group">
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		    	<h1 class="page-header">Other methods</h1>
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				<div id="pre_process" class="subgroup">
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					<h2>Pre process</h2>
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					<p><code>pre_process()</code> is executed before running the <code>process</code> method. Unlike <code>process</code>, this method does not allow
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					to add components, but can be useful when implementing an application requiring to prepare some data before running the workflow (insert / recover
					information from a database, add metadata to the workflow, ...).</p>
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				</div>
				<div id="post_process" class="subgroup">
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					<h2>Post process</h2>
					<p><code>post_process()</code> is executed right after the <code>process</code> method and cannot be used to add components. This method can
					be useful to perform some database transactions and to synchronize data.</p>
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				</div>
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				<div id="set_to_address" class="subgroup">
					<h2>Set to address</h2>
					<p><code>set_to_address()</code> overwrite the value <code>to_address</code> defined in the jflow configuration file.</p>
	   				<h3>Options</h3>
	   				<p>There is one required argument : to_address.</p>
	   				<div class="table-responsive">
						<table class="table table-bordered table-striped">
							<thead>
								<tr>
									<th>Name</th>
									<th>Type</th>
									<th>Required</th>
									<th>Default value</th>
									<th>Description</th>
								</tr>
							</thead>
							<tbody>
								<tr>
									<td>to_address</td>
									<td>string</td>
									<td>true</td>
									<td>None</td>
									<td>The email address to use to send an email to the user once the workflow is completed.</td>
								</tr>
							</tbody>
						</table>
					</div>
					
				</div>
				<div id="set_subject" class="subgroup">
					<h2>Set email subject</h2>
					<p><code>set_subject()</code> </code> overwrite the value <code>subject</code> defined in the jflow configuration file.</p>
	   				<h3>Options</h3>
	   				<p>There is one required argument : subject.</p>
	   				<div class="table-responsive">
						<table class="table table-bordered table-striped">
							<thead>
								<tr>
									<th>Name</th>
									<th>Type</th>
									<th>Required</th>
									<th>Default value</th>
									<th>Description</th>
								</tr>
							</thead>
							<tbody>
								<tr>
									<td>subject</td>
									<td>string</td>
									<td>true</td>
									<td>None</td>
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									<td>The email subject to use for the email sent to the user once the workflow is completed.<br />
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									Placeholders can be used to access workflow attributes or unparametred methods: 
									<code>###attribute###</code> or <code>###method()###</code>. For timestamps you can apply 
									date function with the following syntax: <code>###attribute|date###</code> or <code>###method()|date###"</code>.
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									</td>
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								</tr>
							</tbody>
						</table>
					</div>
				</div>
				<div id="set_message" class="subgroup">
					<h2>Set email message</h2>
					<p><code>set_message()</code> overwrite the value <code>message</code> defined in the jflow configuration file.</p>
	   				<h3>Options</h3>
	   				<p>There is one required argument : message.</p>
	   				<div class="table-responsive">
						<table class="table table-bordered table-striped">
							<thead>
								<tr>
									<th>Name</th>
									<th>Type</th>
									<th>Required</th>
									<th>Default value</th>
									<th>Description</th>
								</tr>
							</thead>
							<tbody>
								<tr>
									<td>message</td>
									<td>string</td>
									<td>true</td>
									<td>None</td>
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									<td>The email message to use for the email sent to the user once the workflow is completed.<br />
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									Placeholders can be used to access workflow attributes or unparametred methods: 
									<code>###attribute###</code> or <code>###method()###</code>. For timestamps you can apply 
									date function with the following syntax: <code>###attribute|date###</code> or <code>###method()|date###"</code>.
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									</td>
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								</tr>
							</tbody>
						</table>
					</div>
				</div>
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				<div id="get_resource" class="subgroup">
					<h2>Get shared resources</h2>
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					<p>The method <code>get_resource()</code>, giving a specific resource, returns the defined value within the <code>resources</code>
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					section of the jflow configuration file.</p>
	   				<h3>Options</h3>
	   				<p>There is one required argument : resource.</p>
	   				<div class="table-responsive">
						<table class="table table-bordered table-striped">
							<thead>
								<tr>
									<th>Name</th>
									<th>Type</th>
									<th>Required</th>
									<th>Default value</th>
									<th>Description</th>
								</tr>
							</thead>
							<tbody>
								<tr>
									<td>resource</td>
									<td>string</td>
									<td>true</td>
									<td>None</td>
									<td>The resource name for which is requested the configured value.</td>
								</tr>
							</tbody>
						</table>
					</div>
				</div>
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			</section>
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			<section id="your-rules" class="group">
				<h1 class="page-header">Create your own parameter rules</h1>

				<p>You can create your own custom parameter rules. These rules must be declared into the file
					<code>workflows/rules.py</code>. In this file, you define the rule checking protocol. Into the
				parameter definition, the rule is set as a string describing the rule (see below).</p>

				<p>Their are three types of rules : simple rules, link rules and conditional link rules.
				</p>

				<div id="simple-rules" class="subgroup">
					<h2>Simple rules</h2>

					<p>Simple rules are declared as a simple word in the rule definition of the parameter. Example: <code>Unique</code>.
					This name is the name of the class declared below (case-sensitive).</p>
					<p>To create a such rule, create a class that inherit from the SimpleRule class:</p>
					<div>
				    		<pre class="pre-hl "><code class="python">class YourRule (SimpleRule):
	def check():
		# Your code</code></pre>
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