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1 <tool id="GetSizes" name="get sizes">
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2 <description>Get the sizes of a set of genomic coordinates.</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">
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7 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
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8
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9 #if $OptionQuery.OptionQ == 'NONE':
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10 -q size
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11 #else:
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12 $OptionQuery.OptionQ
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13 #end if
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14
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15 -o $outputFile
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16
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17 #if $OptionXMax.xMax == "Yes":
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18 -x $OptionXMax.maxValue
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19 #end if
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20 #if $OptionX.xLab == "Yes":
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21 -a $OptionX.xLabValue
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22 #end if
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23 #if $OptionY.yLab == "Yes":
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24 -b $OptionY.yLabValue
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25 #end if
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26 $barPlot
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27 </command>
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28
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29 <inputs>
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30 <conditional name="formatType">
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31 <param name="FormatInputFileName" type="select" label="Input File Format">
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32 <option value="-f bed">bed</option>
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33 <option value="-f gff">gff</option>
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34 <option value="-f gff2">gff2</option>
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35 <option value="-f gff3">gff3</option>
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36 <option value="-f sam">sam</option>
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37 <option value="-f gtf">gtf</option>
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38 <option value="-f fasta">fasta</option>
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39 <option value="-f fastq">fastq</option>
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40 </param>
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41 <when value="-f bed">
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42 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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43 </when>
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44 <when value="-f gff">
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45 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
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46 </when>
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47 <when value="-f gff2">
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48 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
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49 </when>
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50 <when value="-f gff3">
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51 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
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52 </when>
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53 <when value="-f sam">
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54 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
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55 </when>
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56 <when value="-f gtf">
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57 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
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58 </when>
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59 <when value="-f fasta">
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60 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
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61 </when>
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62 <when value="-f fastq">
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63 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
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64 </when>
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65 </conditional>
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66
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67 <conditional name="OptionQuery">
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68 <param name="OptionQ" type="select" label="mesure type">
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69 <option value="-q size">size</option>
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70 <option value="-q intron size">intron size</option>
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71 <option value="-q exon size">exon size</option>
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72 <option value="-q 1st exon size">1st exon size</option>
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73 <option value="NONE" selected="true">NONE</option>
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74 </param>
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75 <when value="-q size">
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76 </when>
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77 <when value="-q intron size">
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78 </when>
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79 <when value="-q exon size">
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80 </when>
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81 <when value="-q 1st exon size">
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82 </when>
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83 <when value="NONE">
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84
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85 </when>
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86 </conditional>
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87
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88 <conditional name="OptionXMax">
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89 <param name="xMax" type="select" label="maximum x-value to plot">
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90 <option value="Yes">Yes</option>
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91 <option value="No" selected="true">No</option>
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92 </param>
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93 <when value="Yes">
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94 <param name="maxValue" type="integer" value="1000"/>
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95 </when>
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96 <when value="No">
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97 </when>
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98 </conditional>
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99
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100 <conditional name="OptionX">
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101 <param name="xLab" type="select" label="X label title">
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102 <option value="Yes">Yes</option>
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103 <option value="No" selected="true">No</option>
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104 </param>
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105 <when value="Yes">
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106 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
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107 </when>
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108 <when value="No">
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109 </when>
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110 </conditional>
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111
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112 <conditional name="OptionY">
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113 <param name="yLab" type="select" label="Y label title">
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114 <option value="Yes">Yes</option>
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115 <option value="No" selected="true">No</option>
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116 </param>
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117 <when value="Yes">
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118 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
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119 </when>
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120 <when value="No">
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121 </when>
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122 </conditional>
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123
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124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
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125 </inputs>
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126
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127 <outputs>
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128 <data name="outputFile" format="png" label="[get sizes] output file"/>
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129 </outputs>
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130
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131 <help>
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132 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
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133
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134 When your mapping include exon/intron structures, you can decide to count the size of the introns, the sizes of the exons or the size of the first exons.
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135 </help>
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136 </tool>
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