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RAPPEL : Opération de maintenance > ForgeMIA indisponible le 20 Janvier entre 7h et 12h

Commit 5d4dbfeb authored by Jerome Mariette's avatar Jerome Mariette
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multi parameter ok

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docs/jflow-core-workflow.html
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......@@ -171,11 +171,10 @@ class MyWorkflow (Workflow):
is added to the workflow. It has a list of choices and the default value is "HiSeq2000".
</p>
<div>
<pre class="pre-hl "><code class="python">def define_parameters(self, function="process"):
self.add_parameter("sequencer",
"The sequencer type.",
choices = ["HiSeq2000", "ILLUMINA","SLX","SOLEXA","454","UNKNOWN"],
default="HiSeq2000")</code></pre>
<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>
</div>
<h4>Options</h4>
......@@ -250,7 +249,7 @@ class MyWorkflow (Workflow):
<td>string</td>
<td>false</td>
<td>None</td>
<td>The command line flag (if the value is None, the flag will be <em>"--name"</em>).</td>
<td>The command line flag (if the value is None, the flag will be <code>--name</code>).</td>
</tr>
<tr>
......@@ -305,11 +304,10 @@ class MyWorkflow (Workflow):
is added to the workflow. The provided file is required and should be in fastq format. No file size limitation is specified.
</p>
<div>
<pre class="pre-hl "><code class="python">def define_parameters(self, function="process"):
self.add_input_file_list("reads",
"Which read files should be used",
file_format="fastq",
required=True)</code></pre>
<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>
</div>
<h4>Options</h4>
......@@ -388,7 +386,7 @@ class MyWorkflow (Workflow):
<td>string</td>
<td>false</td>
<td>None</td>
<td>The command line flag (if the value is None, the flag will be <em>"--name"</em>).</td>
<td>The command line flag (if the value is None, the flag will be <code>--name</code>).</td>
</tr>
<tr>
......@@ -440,9 +438,19 @@ class MyWorkflow (Workflow):
<div id="multiple_parameters" class="subgroup">
<h2>Multiple parameters</h2>
<p>A multiple parameter can be viewed as python dictionary containing different type of parameter. The next 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>
<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>
<div>
<pre class="pre-hl "><code class="python">self.add_multiple_parameter("library", "Library.", required=True)
......@@ -451,15 +459,9 @@ self.add_input_file("R2", "Path to R2 file.", add_to="library")
self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
"ILLUMINA", "UNKNOWN"], default="HiSeq2000", add_to="library")</code></pre>
</div>
<h3>how to populate a multiple parameter</h3>
<p>To add a parameter in the multiple parameter, use the option <code>add_to</code>. See the previous options.</p>
<h3>add_multiple_parameter()</h3>
<h4>Options</h4>
<p>There are two positional options name and help, other options can be added as keyword options.</p>
<h4>Options</h4>
<p>There are two positional argument : name and help. All other options are keyword options.</p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
......@@ -478,7 +480,9 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<td>string</td>
<td>true</td>
<td>None</td>
<td>The name of the parameter.</td>
<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>
</tr>
<tr>
......@@ -486,7 +490,7 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<td>string</td>
<td>true</td>
<td>None</td>
<td>The help message pronpted to the user.</td>
<td>The parameter help message.</td>
</tr>
<tr>
......@@ -502,7 +506,8 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<td>string</td>
<td>false</td>
<td>None</td>
<td>The parameter command line flag (default is <em>"--name"</em>).</td>
<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>
</tr>
<tr>
......@@ -510,7 +515,7 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<td>string</td>
<td>false</td>
<td>"default"</td>
<td>This is used to regroup a list of parameters in the command line and the GUI.</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>
......@@ -518,24 +523,35 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<td>string</td>
<td>false</td>
<td>None</td>
<td>The display name of the parameter.</td>
<td>The parameter name that should be displayed on the final form.</td>
</tr>
</tbody>
</table>
</div>
<h3>add_multiple_parameter_list()</h3>
<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>
<p>This method adds a parameter which is a list of multiple parameter. The definition and options for this
method are the same as <code>add_multiple_parameter()</code> </p>
</div>
<div id="exclusion_rules" class="subgroup">
<h2>Exclusion rules</h2>
<p>An exclusion rules allows to set parameters as excluded from each other. The method <code>add_exclusion_rule()</code> is used. </p>
<p>Jflow offers the possibility to exclude some rules from each otehrs. To do so, the method <code>add_exclusion_rule()</code> is available. </p>
<h3>add_exclution_rule()</h3>
<h4>Example</h4>
<p>In the following example, the final user will not be allowed to provide both <code>fasta_file</code> and <code>fastq_file</code> parameters.</p>
<div>
<pre class="pre-hl "><code class="python">self.add_input_file("fasta_file", "Path to the fasta file.", format="fasta")
self.add_input_file("fastq_file", "Path to the fastq file.", format="fastq")
self.add_exclution_rule("fasta_file", "fastq")</code></pre>
</div>
<h4>Options</h4>
<p>The method accept the following options</p>
<div class="table-responsive">
......
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