mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
40 lines
1.9 KiB
XML
40 lines
1.9 KiB
XML
<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
|
|
<!-- output contains file location info, commented out functional tests -->
|
|
<description>Find protein sequence regions with a biased composition</description>
|
|
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
<command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
|
|
<inputs>
|
|
<param format="data" name="input1" type="data">
|
|
<label>Sequences</label>
|
|
</param>
|
|
<param format="data" name="input2" type="data">
|
|
<label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
|
|
</param>
|
|
<param name="window" size="4" type="text" value="30">
|
|
<label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
|
|
</param>
|
|
<param name="ignorebz" type="select">
|
|
<label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words
|
|
containing them, just noting them in the count of 'Other' words</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="oddcomp" name="out_file1" />
|
|
</outputs>
|
|
<!-- <tests>
|
|
<test>
|
|
<param name="input1" value="2.fasta"/>
|
|
<param name="input2" value="emboss_compseq_out.compseq"/>
|
|
<param name="window" value="30"/>
|
|
<param name="ignorebz" value="yes"/>
|
|
<output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
|
|
</test>
|
|
</tests> -->
|
|
<help>
|
|
You can view the original documentation here_.
|
|
|
|
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html
|
|
</help>
|
|
</tool> |