/tools/emboss_5/emboss_twofeat.xml
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1<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0"> 2 <description>Finds neighbouring pairs of features in sequences</description> 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" 5 -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap 6 -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command> 7 <inputs> 8 <param format="data" name="input1" type="data"> 9 <label>Sequences</label> 10 </param> 11 <param name="atype" size="50" type="text" value="*"> 12 <label>Feature type you wish to allow. Feature 1</label> 13 </param> 14 <param name="btype" size="50" type="text" value="*"> 15 <label>Feature type you wish to allow. Feature 2</label> 16 </param> 17 <param name="minrange" size="5" type="text" value="0"> 18 <label>Minimun range</label> 19 </param> 20 <param name="maxrange" size="5" type="text" value="0"> 21 <label>Maximum range</label> 22 </param> 23 <param name="asource" size="50" type="text" value="*"> 24 <label>Feature source 1</label> 25 </param> 26 <param name="asense" type="select"> 27 <label>Feature sense 1</label> 28 <option value="0">Any sense</option> 29 <option value="+">Forward sense</option> 30 <option value="-">Reverse sense</option> 31 </param> 32 <param name="aminscore" size="5" type="text" value="0.0"> 33 <label>Feature 1 minimum score</label> 34 </param> 35 <param name="amaxscore" size="5" type="text" value="0.0"> 36 <label>Feature1 maxiumum score</label> 37 </param> 38 <param name="atag" size="50" type="text" value="*"> 39 <label>Feature 1 tag</label> 40 </param> 41 <param name="avalue" size="50" type="text" value="*"> 42 <label>Tag 1 value</label> 43 </param> 44 <param name="bsource" size="50" type="text" value="*"> 45 <label>Feature 2 source</label> 46 </param> 47 <param name="bsense" type="select"> 48 <label>Feature 2 sense</label> 49 <option value="0">Any sense</option> 50 <option value="+">Forward sense</option> 51 <option value="-">Reverse sense</option> 52 </param> 53 <param name="bminscore" size="5" type="text" value="0.0"> 54 <label>Feature 2 miniumum score</label> 55 </param> 56 <param name="bmaxscore" size="5" type="text" value="0.0"> 57 <label>Feature 2 maximum score</label> 58 </param> 59 <param name="btag" size="50" type="text" value="*"> 60 <label>Feature 2 tag</label> 61 </param> 62 <param name="bvalue" size="50" type="text" value="*"> 63 <label>Feature 2 tag value</label> 64 </param> 65 <param name="overlap" type="select"> 66 <label>opverlaps allowed</label> 67 <option value="A">Any</option> 68 <option value="O">Overlap required but not within</option> 69 <option value="NO">No overlaps are allowed</option> 70 <option value="NW:">Overlap required but not within</option> 71 <option value="AW">A must be all within B</option> 72 <option value="BW">B must be all within A</option> 73 </param> 74 <param name="rangetype" type="select"> 75 <label>How to determine range</label> 76 <option value="N">From nearest ends</option> 77 <option value="L">From left ends</option> 78 <option value="R">From right ends</option> 79 <option value="F">From furthest ends</option> 80 </param> 81 <param name="sense" type="select"> 82 <label>Required sense</label> 83 <option value="A">Any sense</option> 84 <option value="S">Same sense</option> 85 <option value="O">Opposite sense</option> 86 </param> 87 <param name="order" type="select"> 88 <label>Required order of the two features</label> 89 <option value="A">Any</option> 90 <option value="AB">Feature A then feature B</option> 91 <option value="BA">Feature B then feature A</option> 92 </param> 93 <param name="twoout" type="select"> 94 <label>Write out the two features themselves</label> 95 <option value="no">No</option> 96 <option value="yes">Yes</option> 97 </param> 98 <param name="typeout" size="50" type="text" value="misc_feature"> 99 <label>New feature type</label> 100 </param> 101 <param name="out_format1" type="select"> 102 <label>Output Report File Format</label> 103 <option value="table">Table</option> 104 <option value="embl">EMBL</option> 105 <option value="genbank">GENBANK</option> 106 <option value="gff">GFF</option> 107 <option value="pir">PIR</option> 108 <option value="swiss">SwissProt</option> 109 <option value="dbmotif">DbMotif</option> 110 <option value="diffseq">Diffseq</option> 111 <option value="excel">Excel (tab delimited)</option> 112 <option value="feattable">FeatTable</option> 113 <option value="motif">Motif</option> 114 <option value="regions">Regions</option> 115 <option value="seqtable">SeqTable</option> 116 <option value="simple">SRS Simple</option> 117 <option value="srs">SRS</option> 118 <option value="tagseq">TagSeq</option> 119 </param> 120 </inputs> 121 <outputs> 122 <data format="table" name="out_file1" /> 123 </outputs> 124 <code file="emboss_format_corrector.py" /> 125 <help> 126 You can view the original documentation here_. 127 128 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html 129 130------ 131 132**Citation** 133 134If 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>`_ 135 </help> 136</tool>