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6
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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 <command interpreter="python">
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4 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
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5
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6 #if $OptionQuery.OptionQ == 'NONE':
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7 -q size
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8 #else:
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9 $OptionQuery.OptionQ
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10 #end if
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11
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12 -o $outputFile
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13
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14 #if $OptionXMax.xMax == "Yes":
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15 -x $OptionXMax.maxValue
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16 #end if
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17 #if $OptionX.xLab == "Yes":
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18 -a $OptionX.xLabValue
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19 #end if
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20 #if $OptionY.yLab == "Yes":
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21 -b $OptionY.yLabValue
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22 #end if
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23 $barPlot
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31
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24 $excel $excelOutput
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6
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25 </command>
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26
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27 <inputs>
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28 <conditional name="formatType">
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29 <param name="FormatInputFileName" type="select" label="Input File Format">
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30 <option value="-f bed">bed</option>
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31 <option value="-f gff">gff</option>
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32 <option value="-f gff2">gff2</option>
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33 <option value="-f gff3">gff3</option>
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34 <option value="-f sam">sam</option>
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35 <option value="-f gtf">gtf</option>
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36 <option value="-f fasta">fasta</option>
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37 <option value="-f fastq">fastq</option>
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38 </param>
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39 <when value="-f bed">
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40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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41 </when>
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42 <when value="-f gff">
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43 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
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44 </when>
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45 <when value="-f gff2">
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46 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
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47 </when>
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48 <when value="-f gff3">
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49 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
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50 </when>
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51 <when value="-f sam">
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52 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
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53 </when>
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54 <when value="-f gtf">
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55 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
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56 </when>
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57 <when value="-f fasta">
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58 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
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59 </when>
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60 <when value="-f fastq">
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61 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
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62 </when>
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63 </conditional>
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64
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65 <conditional name="OptionQuery">
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66 <param name="OptionQ" type="select" label="mesure type">
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67 <option value="-q size">size</option>
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68 <option value="-q intron size">intron size</option>
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69 <option value="-q exon size">exon size</option>
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70 <option value="-q 1st exon size">1st exon size</option>
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71 <option value="NONE" selected="true">NONE</option>
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72 </param>
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73 <when value="-q size">
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74 </when>
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75 <when value="-q intron size">
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76 </when>
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77 <when value="-q exon size">
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78 </when>
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79 <when value="-q 1st exon size">
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80 </when>
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81 <when value="NONE">
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82
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83 </when>
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84 </conditional>
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85
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86 <conditional name="OptionXMax">
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87 <param name="xMax" type="select" label="maximum value on the x-axis to plot [format: int]">
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88 <option value="Yes">Yes</option>
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89 <option value="No" selected="true">No</option>
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90 </param>
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91 <when value="Yes">
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92 <param name="maxValue" type="integer" value="1000"/>
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93 </when>
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94 <when value="No">
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95 </when>
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96 </conditional>
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97
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98 <conditional name="OptionX">
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99 <param name="xLab" type="select" label="X label title">
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100 <option value="Yes">Yes</option>
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101 <option value="No" selected="true">No</option>
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102 </param>
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103 <when value="Yes">
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104 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
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105 </when>
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106 <when value="No">
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107 </when>
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108 </conditional>
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109
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110 <conditional name="OptionY">
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111 <param name="yLab" type="select" label="Y label title">
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112 <option value="Yes">Yes</option>
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113 <option value="No" selected="true">No</option>
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114 </param>
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115 <when value="Yes">
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116 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
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117 </when>
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118 <when value="No">
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119 </when>
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120 </conditional>
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121
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31
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122
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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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31
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125
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126 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
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6
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127 </inputs>
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128
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129 <outputs>
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31
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130 <data name="outputFile" format="png" label="[Get sizes] output file"/>
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131 <data name="excelOutput" format="csv">
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132 <filter>excel</filter>
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133 </data>
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6
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134 </outputs>
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135 </tool>
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