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1 <tool id="restrictTranscriptList" name="restrict transcript list">
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2 <description>Select the features which are located in a given locus.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName
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7 #if $formatType.FormatInputFileName == 'bed':
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8 -f bed
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9 #elif $formatType.FormatInputFileName == 'gff':
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10 -f gff
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11 #elif $formatType.FormatInputFileName == 'gff2':
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12 -f gff2
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13 #elif $formatType.FormatInputFileName == 'gff3':
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14 -f gff3
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15 #elif $formatType.FormatInputFileName == 'sam':
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16 -f sam
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17 #elif $formatType.FormatInputFileName == 'gtf':
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18 -f gtf
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19 #end if
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20
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21 #if $OptionChrom.Chrom == "Yes":
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22 -c $OptionChrom.ChromName
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23 #end if
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24
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25 #if $OptionStart.start == "Yes":
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26 -s $OptionStart.startValue
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27 #end if
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28
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29 #if $OptionEnd.end == "Yes":
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30 -e $OptionEnd.endValue
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31 #end if
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32
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33 -o $outputFile
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34
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35 </command>
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36
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37
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38 <inputs>
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39 <conditional name="formatType">
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40 <param name="FormatInputFileName" type="select" label="Input File Format">
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41 <option value="bed">bed</option>
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42 <option value="gff">gff</option>
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43 <option value="gff2">gff2</option>
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44 <option value="gff3">gff3</option>
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45 <option value="sam">sam</option>
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46 <option value="gtf">gtf</option>
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47 </param>
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48 <when value="bed">
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49 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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50 </when>
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51 <when value="gff">
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52 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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53 </when>
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54 <when value="gff2">
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55 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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56 </when>
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57 <when value="gff3">
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58 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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59 </when>
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60 <when value="sam">
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61 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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62 </when>
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63 <when value="gtf">
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64 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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65 </when>
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66 </conditional>
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67
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68 <conditional name="OptionChrom">
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69 <param name="Chrom" type="select" label="chromosome name">
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70 <option value="Yes">Yes</option>
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71 <option value="No" selected="true">No</option>
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72 </param>
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73 <when value="Yes">
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74 <param name="ChromName" type="text" value="None"/>
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75 </when>
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76 <when value="No">
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77 </when>
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78 </conditional>
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79
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80 <conditional name="OptionStart">
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81 <param name="start" type="select" label="start region of the locus">
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82 <option value="Yes">Yes</option>
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83 <option value="No" selected="true">No</option>
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84 </param>
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85 <when value="Yes">
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86 <param name="startValue" type="integer" value="0"/>
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87 </when>
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88 <when value="No">
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89 </when>
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90 </conditional>
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91
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92 <conditional name="OptionEnd">
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93 <param name="end" type="select" label="end region of the locus">
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94 <option value="Yes">Yes</option>
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95 <option value="No" selected="true">No</option>
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96 </param>
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97 <when value="Yes">
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98 <param name="endValue" type="integer" value="0"/>
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99 </when>
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100 <when value="No">
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101 </when>
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102 </conditional>
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103 </inputs>
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104
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105 <outputs>
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106 <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/>
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107 </outputs>
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108
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109 <help>
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110 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
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111 </help>
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112 <tests>
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113 <test>
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114 <param name="FormatInputFileName" value="gtf" />
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115 <param name="inputFileName" value="genes.gtf" />
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116 <param name="Chrom" value="Yes"/>
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117 <param name="ChromName" value="I"/>
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118 <param name="start" value="No" />
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119 <param name="end" value="No" />
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120 <output name="outputFile" file="exp_restrictTranscriptList.gff3" />
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121 </test>
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122 </tests>
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123
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124 </tool>
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