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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> |
