38
+ − 1 <tool id="GetSizes" name="get sizes">
+ − 2 <description>Get the sizes of a set of genomic coordinates.</description>
+ − 3 <requirements>
+ − 4 <requirement type="set_environment">PYTHONPATH</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python">
+ − 7 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
+ − 8
+ − 9 #if $OptionQuery.OptionQ == 'NONE':
+ − 10 -q size
+ − 11 #else:
+ − 12 $OptionQuery.OptionQ
+ − 13 #end if
+ − 14
+ − 15 -o $outputFile
+ − 16
+ − 17 #if $OptionXMax.xMax == "Yes":
+ − 18 -x $OptionXMax.maxValue
+ − 19 #end if
+ − 20 #if $OptionX.xLab == "Yes":
+ − 21 -a $OptionX.xLabValue
+ − 22 #end if
+ − 23 #if $OptionY.yLab == "Yes":
+ − 24 -b $OptionY.yLabValue
+ − 25 #end if
+ − 26 $barPlot
+ − 27 </command>
+ − 28
+ − 29 <inputs>
+ − 30 <conditional name="formatType">
+ − 31 <param name="FormatInputFileName" type="select" label="Input File Format">
+ − 32 <option value="-f bed">bed</option>
+ − 33 <option value="-f gff">gff</option>
+ − 34 <option value="-f gff2">gff2</option>
+ − 35 <option value="-f gff3">gff3</option>
+ − 36 <option value="-f sam">sam</option>
+ − 37 <option value="-f gtf">gtf</option>
+ − 38 <option value="-f fasta">fasta</option>
+ − 39 <option value="-f fastq">fastq</option>
+ − 40 </param>
+ − 41 <when value="-f bed">
+ − 42 <param name="inputFileName" format="bed" type="data" label="Input File"/>
+ − 43 </when>
+ − 44 <when value="-f gff">
+ − 45 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
+ − 46 </when>
+ − 47 <when value="-f gff2">
+ − 48 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
+ − 49 </when>
+ − 50 <when value="-f gff3">
+ − 51 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
+ − 52 </when>
+ − 53 <when value="-f sam">
+ − 54 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
+ − 55 </when>
+ − 56 <when value="-f gtf">
+ − 57 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
+ − 58 </when>
+ − 59 <when value="-f fasta">
+ − 60 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
+ − 61 </when>
+ − 62 <when value="-f fastq">
+ − 63 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
+ − 64 </when>
+ − 65 </conditional>
+ − 66
+ − 67 <conditional name="OptionQuery">
+ − 68 <param name="OptionQ" type="select" label="mesure type">
+ − 69 <option value="-q size">size</option>
+ − 70 <option value="-q intron size">intron size</option>
+ − 71 <option value="-q exon size">exon size</option>
+ − 72 <option value="-q 1st exon size">1st exon size</option>
+ − 73 <option value="NONE" selected="true">NONE</option>
+ − 74 </param>
+ − 75 <when value="-q size">
+ − 76 </when>
+ − 77 <when value="-q intron size">
+ − 78 </when>
+ − 79 <when value="-q exon size">
+ − 80 </when>
+ − 81 <when value="-q 1st exon size">
+ − 82 </when>
+ − 83 <when value="NONE">
+ − 84
+ − 85 </when>
+ − 86 </conditional>
+ − 87
+ − 88 <conditional name="OptionXMax">
+ − 89 <param name="xMax" type="select" label="maximum x-value to plot">
+ − 90 <option value="Yes">Yes</option>
+ − 91 <option value="No" selected="true">No</option>
+ − 92 </param>
+ − 93 <when value="Yes">
+ − 94 <param name="maxValue" type="integer" value="1000"/>
+ − 95 </when>
+ − 96 <when value="No">
+ − 97 </when>
+ − 98 </conditional>
+ − 99
+ − 100 <conditional name="OptionX">
+ − 101 <param name="xLab" type="select" label="X label title">
+ − 102 <option value="Yes">Yes</option>
+ − 103 <option value="No" selected="true">No</option>
+ − 104 </param>
+ − 105 <when value="Yes">
+ − 106 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
+ − 107 </when>
+ − 108 <when value="No">
+ − 109 </when>
+ − 110 </conditional>
+ − 111
+ − 112 <conditional name="OptionY">
+ − 113 <param name="yLab" type="select" label="Y label title">
+ − 114 <option value="Yes">Yes</option>
+ − 115 <option value="No" selected="true">No</option>
+ − 116 </param>
+ − 117 <when value="Yes">
+ − 118 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
+ − 119 </when>
+ − 120 <when value="No">
+ − 121 </when>
+ − 122 </conditional>
+ − 123
+ − 124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
+ − 125 </inputs>
+ − 126
+ − 127 <outputs>
+ − 128 <data name="outputFile" format="png" label="[get sizes] output file"/>
+ − 129 </outputs>
+ − 130
+ − 131 <help>
+ − 132 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
+ − 133
+ − 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.
+ − 135 </help>
+ − 136 </tool>
