Mercurial > repos > devteam > emboss_5
diff emboss_twofeat.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
line wrap: on
line diff
--- a/emboss_twofeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_twofeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,138 +1,94 @@ -<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0"> - <description>Finds neighbouring pairs of features in sequences</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <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 format="data" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="atype" type="text" value="*"> - <label>Feature type you wish to allow. Feature 1</label> - </param> - <param name="btype" type="text" value="*"> - <label>Feature type you wish to allow. Feature 2</label> - </param> - <param name="minrange" type="text" value="0"> - <label>Minimun range</label> - </param> - <param name="maxrange" type="text" value="0"> - <label>Maximum range</label> - </param> - <param name="asource" type="text" value="*"> - <label>Feature source 1</label> - </param> - <param name="asense" type="select"> - <label>Feature sense 1</label> - <option value="0">Any sense</option> - <option value="+">Forward sense</option> - <option value="-">Reverse sense</option> - </param> - <param name="aminscore" type="text" value="0.0"> - <label>Feature 1 minimum score</label> - </param> - <param name="amaxscore" type="text" value="0.0"> - <label>Feature1 maxiumum score</label> - </param> - <param name="atag" type="text" value="*"> - <label>Feature 1 tag</label> - </param> - <param name="avalue" type="text" value="*"> - <label>Tag 1 value</label> - </param> - <param name="bsource" type="text" value="*"> - <label>Feature 2 source</label> - </param> - <param name="bsense" type="select"> - <label>Feature 2 sense</label> - <option value="0">Any sense</option> - <option value="+">Forward sense</option> - <option value="-">Reverse sense</option> - </param> - <param name="bminscore" type="text" value="0.0"> - <label>Feature 2 miniumum score</label> - </param> - <param name="bmaxscore" type="text" value="0.0"> - <label>Feature 2 maximum score</label> - </param> - <param name="btag" type="text" value="*"> - <label>Feature 2 tag</label> - </param> - <param name="bvalue" type="text" value="*"> - <label>Feature 2 tag value</label> - </param> - <param name="overlap" type="select"> - <label>opverlaps allowed</label> - <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</label> - <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</label> - <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</label> - <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</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="typeout" type="text" value="misc_feature"> - <label>New feature type</label> - </param> - <param name="out_format1" type="select"> - <label>Output Report File Format</label> - <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 format="table" name="out_file1" /> - </outputs> - <code file="emboss_format_corrector.py" /> +<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1"> + <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://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>