Mercurial > repos > devteam > emboss_5
diff emboss_twofeat.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_twofeat.xml Fri Aug 12 19:17:10 2016 -0400 @@ -0,0 +1,138 @@ +<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" /> + <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>`_ + </help> +</tool> \ No newline at end of file