Commit b0c6bbdb authored by Jerome Mariette's avatar Jerome Mariette

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parent 966dfd67
......@@ -220,9 +220,9 @@ class MyComponent (Analysis):
</p>
<div>
<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>
"The sequencer type.",
choices = ["HiSeq2000", "ILLUMINA","SLX","SOLEXA","454","UNKNOWN"],
default="HiSeq2000")</code></pre>
</div>
<h4>Options</h4>
......@@ -626,8 +626,8 @@ self.casava_directory.get_files( *args)</code></pre>
</p>
<div>
<pre class="pre-hl "><code class="python">self.add_output_file("databank",
"The indexed databank",
filename=os.path.basename(input_fasta))</code></pre>
"The indexed databank",
filename=os.path.basename(input_fasta))</code></pre>
</div>
<h4>Options</h4>
......@@ -724,9 +724,9 @@ self.casava_directory.get_files( *args)</code></pre>
</p>
<div>
<pre class="pre-hl "><code class="python">self.add_output_file_list("sam_files",
"The BWA output files",
pattern='{basename_woext}.sam',
items=self.reads)</code></pre>
"The BWA output files",
pattern='{basename_woext}.sam',
items=self.reads)</code></pre>
</div>
<h4>Options</h4>
......@@ -835,9 +835,10 @@ self.casava_directory.get_files( *args)</code></pre>
<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>
In the following example, an output named <code>sam_files</code>
......@@ -848,8 +849,8 @@ self.casava_directory.get_files( *args)</code></pre>
<div>
<pre class="pre-hl "><code class="python">self.add_output_file_endswith("sam_files",
"The BWA output files",
pattern='.sam')</code></pre>
"The BWA output files",
pattern='.sam')</code></pre>
</div>
<h4>Options</h4>
......@@ -953,10 +954,10 @@ self.casava_directory.get_files( *args)</code></pre>
<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>
In the following example, an output named <code>sam_files</code>
......@@ -967,8 +968,8 @@ self.casava_directory.get_files( *args)</code></pre>
<div>
<pre class="pre-hl "><code class="python">self.add_output_file_pattern("sam_files",
"The BWA output files",
pattern='*_R1.sam')</code></pre>
"The BWA output files",
pattern='*_R1.sam')</code></pre>
</div>
<h4>Options</h4>
......
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