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<tool id="odosenl_run_orthomcl" name="Identify core set of single copy ortholog genes">
<description>using OrthoMCL to find orthologs using reciprocal BLAST and HMM clustering</description>
<command interpreter="python">wrapper.py run_orthomcl $logfile
$proteinzip
--poorlength $proteinlength
--evalue $evalueexponent
$poorproteins
$groups
</command>
<inputs>
<param format="faa.zip" name="proteinzip" type="data" label="Translated gene proteins" />
<param name="proteinlength" type="integer" label="Minimum protein length" min="0" value="30" optional="false">
<help>Proteins shorter than this length will be considers poor proteins and filtered out by OrthoMCL.</help>
</param>
<param name="evalueexponent" type="integer" label="OrthoMCL expect value exponent cut-off" value="-5" optional="false">
<help>OrthoMCL BLAST similarities with Expect value exponents greater than this value are ignored. See BLAST and OrthoMCL documentation for more details.</help>
</param>
</inputs>
<outputs>
<data format="txt" name="logfile" label="OrthoMCL logfile" />
<data format="fasta" name="poorproteins" label="List of excluded proteins (&lt;${proteinlength} AA)" />
<data format="groups.tsv" name="groups" label="Overview of all orthologs" />
</outputs>
<help>
This tool runs OrthoMCL (http://www.orthomcl.org) and returns the orthologous groups file.
</help>
</tool>