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view emboss_wordmatch.xml @ 13:d5c3794bd246 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author | iuc |
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date | Mon, 23 Apr 2018 13:04:47 -0400 |
parents | 0e2484b6829b |
children | 27c43fb015f0 |
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<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0.1"> <description>Finds all exact matches of a given size between 2 sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command> <inputs> <param name="input1" type="data" format="fasta" label="Sequence 1" /> <param name="input2" type="data" format="fasta" label="Sequence 2" /> <param name="wordsize" type="integer" value="4" label="Word size" /> <param name="out_format1" type="select" label="Output alignment file format"> <option value="match">Match (m)</option> <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> <param name="out_format2" type="select" label="Output feature 1 file format"> <option value="gff">GFF</option> <option value="embl">EMBL</option> <option value="swiss">SwissProt</option> </param> <param name="out_format3" type="select" label="Output feature 2 file format"> <option value="gff">GFF</option> <option value="embl">EMBL</option> <option value="swiss">SwissProt</option> </param> </inputs> <outputs> <data name="out_file1" format="match" /> <data name="out_file2" format="gff" /> <data name="out_file3" format="gff" /> </outputs> <!-- <tests> <test> <param name="input1" value="2.fasta"/> <param name="input2" value="1.fasta"/> <param name="wordsize" value="4"/> <param name="out_format1" value="fasta"/> <param name="out_format2" value="gff"/> <param name="out_format3" value="gff"/> <output name="ofile2" file="emboss_wordmatch_out.embl"/> </test> </tests> test takes a long time to run--> <help> .. class:: warningmark The input datasets need to be sequences. ----- You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordmatch.html </help> <expand macro="citations" /> </tool>