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

Commit 15c74f57 authored by Philippe Bardou's avatar Philippe Bardou
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Alert div

Handsonetable width 695px!
parent ff44db24
......@@ -672,8 +672,10 @@ class MyComponent (Component):
<h3>add_output_file_endswith()</h3>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
<div class="alert alert-info" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
</div>
<h4>Example</h4>
<p>
......@@ -791,9 +793,10 @@ class MyComponent (Component):
<h3>add_output_file_pattern()</h3>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
<div class="alert alert-info" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
This method should only be used with components producing unknown number of outputs (like some demultiplexing tools).
</div>
<h4>Example</h4>
<p>
......@@ -851,13 +854,14 @@ class MyComponent (Component):
<code>ShellFunction</code> and <code>PythonFunction</code> and two main abstractions: <code>Map</code> and
<code>MultiMap</code>.</p>
<p>
<div class="alert alert-info" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true" ></span>
Overloading <code>process()</code> can be omitted. Jflow offers, for components with easy command lines,
an automatic built of the <code>process()</code> method.
In this case, options <code>argpos</code> and <code>cmd_format</code> must be provided by the developper for each parameter.
Also, two other methods of <code>jflow.component.Component</code> must be overloaded. <code>get_command()</code>, which must returns
the execution path and <code>get_abstraction()</code> which returns the abstraction name to use.</p>
In this case, options <code>argpos</code> and <code>cmd_format</code> must be provided by the developper for each parameter.
Also, two other methods of <code>jflow.component.Component</code> must be overloaded. <code>get_command()</code>, which must returns
the execution path and <code>get_abstraction()</code> which returns the abstraction name to use.
</div>
<div id="functions" class="subgroup">
......@@ -1304,12 +1308,15 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
<p>The method <code>build_component()</code> must be used to return the new component type.The newly created component type must
have a definition of <code>define_parameters()</code>. If the <code>process()</code> method is not redefined, the developper has to overload
<code>get_abstraction()</code> and <code>get_command()</code>. See <a href="#process">process</a> for more details. </p>
<p>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Jflow provides <code>extparsers.mobyle.MobyleParser</code> class as an example to integrate new external component parsers. Adding this class
the developper can add mobyle components, defined by an XML file, by copying the XML definition of the component in any jflow <code>components</code>
packages.
</p>
<p>
<div class="alert alert-info" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Jflow provides <code>extparsers.mobyle.MobyleParser</code> class as an example to integrate new external component parsers. Adding this class
the developper can add mobyle components, defined by an XML file, by copying the XML definition of the component in any jflow <code>components</code>
packages.
</div>
<h3>parse()</h3>
<p>The <code>parse()</code> function is the only function to implement. This function will be called by jflow
and will be executed on any file present in jflow <code>components</code> packages not recognized as an internal
......
......@@ -170,9 +170,10 @@ class MyWorkflow (Workflow):
arguments: <code>name</code> and <code>help</code>. The other arguments are optional and can be given to the method by using their
keywords.
</p>
<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 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>
<div id="parameters" class="subgroup">
<h2>Parameters</h2>
......
......@@ -116,9 +116,11 @@
if nb_seq == 10: break
except:
raise jflow.InvalidFormatError("The provided file '" + ifile + "' is not a fasta file!")</code></pre>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Jflow provides <code>jflow.seqio</code> and <code>jflow.featureio</code> libraries where several file formats handler are available.
<div class="alert alert-info" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Jflow provides <code>jflow.seqio</code> and <code>jflow.featureio</code> libraries where several file formats handler are available.
</div>
</section>
<section id="howuse" class="group">
......
......@@ -20,7 +20,9 @@
***************************************************************/
.handsontable {
overflow: auto;
overflow-x: auto;
overflow-y: hidden;
width: 695px;
}
.handsontable td.htInvalid {
background-image: linear-gradient(to bottom, #d9534f 0px, #c12e2a 100%) !important;
......
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