Mercurial > repos > devteam > emboss_5
view emboss_fuzztran.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: fuzztran39" name="fuzztran" version="@VERSION@.1"> <description>Protein pattern search after translation</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="pattern" type="text" value="" label="Search pattern" /> <param name="mismatch" type="integer" value="0" label="Number of mismatches" /> <param name="frame" type="select" label="Frame(s) to translate"> <option value="1">Frame 1</option> <option value="2">Frame 2</option> <option value="3">Frame 3</option> <option value="F">Forward three frames</option> <option value="-1">Frame -1</option> <option value="-2">Frame -2</option> <option value="-3">Frame -3</option> <option value="R">Reverse three frames</option> <option value="6">All six frames</option> </param> <param name="table" type="select" label="Code to use"> <option value="0">Standard</option> <option value="1">Standard (with alternative initiation codons)</option> <option value="2">Vertebrate Mitochondrial</option> <option value="3">Yeast Mitochondrial</option> <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> <option value="5">Invertebrate Mitochondrial</option> <option value="6">Ciliate Macronuclear and Dasycladacean</option> <option value="9">Echinoderm Mitochondrial</option> <option value="10">Euplotid Nuclear</option> <option value="11">Bacterial</option> <option value="12">Alternative Yeast Nuclear</option> <option value="13">Ascidian Mitochondrial</option> <option value="14">Flatworm Mitochondrial</option> <option value="15">Blepharisma Macronuclear</option> <option value="16">Chlorophycean Mitochondrial</option> <option value="21">Trematode Mitochondrial</option> <option value="22">Scenedesmus obliquus</option> <option value="23">Thraustochytrium Mitochondrial</option> </param> <param name="out_format1" type="select" label="Output report file format"> <option value="table">Table</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="dbmotif">DbMotif</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="tagseq">TagSeq</option> </param> </inputs> <outputs> <data name="out_file1" format="fuzztran" /> </outputs> <tests> <test> <param name="input1" value="1.fasta"/> <param name="pattern" value="AA"/> <param name="mismatch" value="0"/> <param name="frame" value="6"/> <param name="table" value="0"/> <param name="out_format1" value="excel"/> <output name="out_file1" file="emboss_fuzztran_out.tabular"/> </test> </tests> <help> .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzztran.html </help> <expand macro="citations" /> </tool>