Mercurial > repos > devteam > emboss_5
view emboss_patmatdb.xml @ 13:d5c3794bd246 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author | iuc |
---|---|
date | Mon, 23 Apr 2018 13:04:47 -0400 |
parents | 0e2484b6829b |
children | 27c43fb015f0 |
line wrap: on
line source
<tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0"> <description>Search a protein sequence with a motif</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>patmatdb -sequence '$input1' -outfile '$out_file1' -motif '$motif' -rformat3 $out_format1 -auto</command> <inputs> <param name="input1" type="data" format="data" label="Main sequence" /> <param name="motif" type="text" value="" label="Motif to search for" /> <param name="out_format1" type="select" label="Output report file format"> <option value="dbmotif">DbMotif</option> <option value="embl">EMBL</option> <option value="genbank">GENBANK</option> <option value="gff">GFF</option> <option value="pir">PIR</option> <option value="swiss">SwissProt</option> <option value="diffseq">Diffseq</option> <option value="excel">Excel (tab delimited)</option> <option value="feattable">FeatTable</option> <option value="motif">Motif</option> <option value="regions">Regions</option> <option value="seqtable">SeqTable</option> <option value="simple">SRS Simple</option> <option value="srs">SRS</option> <option value="table">Table</option> <option value="tagseq">TagSeq</option> </param> </inputs> <outputs> <data name="out_file1" format="dbmotif" /> </outputs> <tests> <test> <param name="input1" value="2.fasta"/> <param name="motif" value="aa"/> <param name="out_format1" value="excel"/> <output name="out_file1" file="emboss_patmatdb_out.tabular"/> </test> </tests> <help> You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/patmatdb.html </help> <expand macro="citations" /> </tool>