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view emboss_supermatcher.xml @ 16:dba489bfcd62 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit d5dfff2cd58b094e0e4a6f8dc475de5facd9700b"
author | iuc |
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date | Mon, 02 Dec 2019 21:13:50 -0500 |
parents | 8992d258e42f |
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<tool id="EMBOSS: supermatcher95" name="supermatcher" version="@VERSION@.1"> <!-- puts file information in output report --> <description>Match large sequences against one or more other sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3 $out_format1 -auto</command> <inputs> <param name="input1" type="data" format="fasta" label="Large sequences" /> <param name="input2" type="data" format="data" label="Sequences to match" /> <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" /> <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" /> <param name="width" type="integer" value="16" label="Alignment width" /> <param name="wordlen" type="integer" value="6" label="Word length for initial matching" /> <param name="out_format1" type="select" label="Output alignment file format"> <option value="simple">Simple (m)</option> <option value="fasta">FASTA (m)</option> <option value="msf">MSF (m)</option> <option value="srs">SRS (m)</option> <option value="pair">Pair (p)</option> <option value="markx0">Markx0 (p)</option> <option value="markx1">Markx1 (p)</option> <option value="markx2">Markx2 (p)</option> <option value="markx3">Markx3 (p)</option> <option value="markx10">Markx10 (p)</option> <option value="srspair">SRS pair (p)</option> <option value="score">Score (p)</option> </param> </inputs> <outputs> <data name="ofile1" format="simple" /> <data name="ofile2" format="supermatcher" /> </outputs> <!-- <tests> <test> <param name="input1" value="2.fasta"/> <param name="input2" value="1.fasta"/> <param name="gapopen" value="10.0"/> <param name="gapextend" value="0.5"/> <param name="width" value="16"/> <param name="wordlen" value="6"/> <param name="out_format1" value="fasta"/> <output name="ofile1" file="emboss_supermatcher_out.fasta"/> </test> </tests> --> <help> You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/supermatcher.html </help> <expand macro="citations" /> </tool>