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