Commit 82a7b613 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add cutadapt documentation

parent 5efdb254
......@@ -8,14 +8,14 @@
<name>cutadapt</name>
<state>incomplete</state>
<executable>$;CUTADAPT_EXEC$;</executable>
<arg>-e $;ERROR_RATE$; -m $;MIN_LENGTH$; -M $;MAX_LENGTH$; $;OPTIONS$; -o $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.$;COMPONENT_NAME$;.$;I_FILE_EXT$; $;I_FILE_PATH$;</arg>
<arg>-e $;ERROR_RATE$; -m $;MIN_LENGTH$; -M $;MAX_LENGTH$; $;OPTIONS$; -o $;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.$;I_FILE_EXT$; $;I_FILE_PATH$;</arg>
<param>
<key>stdout</key>
<value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.$;COMPONENT_NAME$;.stdout</value>
<value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.stdout</value>
</param>
<param>
<key>stderr</key>
<value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.$;COMPONENT_NAME$;.stat</value>
<value>$;OUTPUT_DIRECTORY$;/$;ITERATOR_NAME$;/g$;GROUP_NUMBER$;/$;I_FILE_BASE$;.stat</value>
</param>
</command>
</commandSet>
......
<p>
From the <a href='http://code.google.com/p/cutadapt/'>cutadapt site</a> :
cutadapt is used to remove adapter sequences from high-throughput sequencing data. This is usually necessary when the
read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
</p>
<blockquote>
<br>
<h3>inputs</h3>
<p>
<ul>
<li></li>
<li>input file: This program accepts fastq files as input.</li>
<li>qual file list: If a fasta file is used as input a qual file can be provided (has to be named input_file.qual or input_file.fasta.qual).</li>
<li>ng6cfg file: The NG6 run config file the analyse belongs to.</li>
<li>project id: The NG6 project id the analyse belongs to.</li>
</ul>
</blockquote>
<h3></h3>
<p>
</p>
<h3></h3>
<h3>outputs</h3>
<p>
Outputs a cleaned file in fastq format and a log file.
</p>
<h3></h3>
<h3>parameters</h3>
<p>
<ul>
<li>min length: Discard trimmed reads that are shorter than LENGTH,</li>
<li>max length: Discard trimmed reads that are longer than LENGTH,</li>
<li>error rate: Maximum allowed error rate,</li>
<li>options: Options for cutadapt ex: -a adaptors,</li>
<li>analyse name: The analyse name to display in ng6,</li>
<li>analyse description: The analyse description to display in ng6,</li>
<li>results archive name: The results archive name to display in ng6.</li>
</ul>
</p>
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment