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view emboss_twofeat.xml @ 17:bde3097ac0f6 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 | Tue, 03 Dec 2019 02:12:56 +0000 |
parents | 27c43fb015f0 |
children | 21a9fb508031 |
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<tool id="EMBOSS: twofeat104" name="twofeat" version="@VERSION@.1"> <description>Finds neighbouring pairs of features in sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange $minrange -maxrange $maxrange -asource '$asource' -asense $asense -aminscore $aminscore -amaxscore $amaxscore -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense $bsense -bminscore $bminscore -bmaxscore $bmaxscore -btag '$btag' -bvalue '$bvalue' -overlap $overlap -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout '$typeout' -rformat2 $out_format1 -auto</command> <inputs> <param name="input1" type="data" format="data" label="Sequences" /> <param name="atype" type="text" value="*" label="Feature type you wish to allow. Feature 1" /> <param name="btype" type="text" value="*" label="Feature type you wish to allow. Feature 2" /> <param name="minrange" type="integer" value="0" label="Minimun range" /> <param name="maxrange" type="integer" value="0" label="Maximum range" /> <param name="asource" type="text" value="*" label="Feature source 1" /> <param name="asense" type="select" label="Feature sense 1"> <option value="0">Any sense</option> <option value="+">Forward sense</option> <option value="-">Reverse sense</option> </param> <param name="aminscore" type="float" value="0.0" label="Feature 1 minimum score" /> <param name="amaxscore" type="float" value="0.0" label="Feature1 maximum score" /> <param name="atag" type="text" value="*" label="Feature 1 tags" /> <param name="avalue" type="text" value="*" label="Feature 1 tag values" /> <param name="bsource" type="text" value="*" label="Feature 2 source" /> <param name="bsense" type="select" label="Feature 2 sense"> <option value="0">Any sense</option> <option value="+">Forward sense</option> <option value="-">Reverse sense</option> </param> <param name="bminscore" type="float" value="0.0" label="Feature 2 minimum score" /> <param name="bmaxscore" type="float" value="0.0" label="Feature 2 maximum score" /> <param name="btag" type="text" value="*" label="Feature 2 tags" /> <param name="bvalue" type="text" value="*" label="Feature 2 tag values" /> <param name="overlap" type="select" label="Allowed overlaps"> <option value="A">Any</option> <option value="O">Overlap required but not within</option> <option value="NO">No overlaps are allowed</option> <option value="NW:">Overlap required but not within</option> <option value="AW">A must be all within B</option> <option value="BW">B must be all within A</option> </param> <param name="rangetype" type="select" label="How to determine range"> <option value="N">From nearest ends</option> <option value="L">From left ends</option> <option value="R">From right ends</option> <option value="F">From furthest ends</option> </param> <param name="sense" type="select" label="Required sense"> <option value="A">Any sense</option> <option value="S">Same sense</option> <option value="O">Opposite sense</option> </param> <param name="order" type="select" label="Required order of the two features"> <option value="A">Any</option> <option value="AB">Feature A then feature B</option> <option value="BA">Feature B then feature A</option> </param> <param name="twoout" type="select" label="Write out the two features themselves"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="typeout" type="text" value="misc_feature" label="New feature type" /> <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="table" /> </outputs> <help> You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html </help> <expand macro="citations" /> </tool>