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comparison SMART/galaxy/getSizes.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="GetSizes" name="get sizes"> 1 <tool id="GetSizes" name="get sizes">
2 <description>Get the sizes of a set of genomic coordinates.</description> 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"> 3 <command interpreter="python">
7 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName 4 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
8 5
9 #if $OptionQuery.OptionQ == 'NONE': 6 #if $OptionQuery.OptionQ == 'NONE':
10 -q size 7 -q size
22 #end if 19 #end if
23 #if $OptionY.yLab == "Yes": 20 #if $OptionY.yLab == "Yes":
24 -b $OptionY.yLabValue 21 -b $OptionY.yLabValue
25 #end if 22 #end if
26 $barPlot 23 $barPlot
24 $excel $excelOutput
27 </command> 25 </command>
28 26
29 <inputs> 27 <inputs>
30 <conditional name="formatType"> 28 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format"> 29 <param name="FormatInputFileName" type="select" label="Input File Format">
84 82
85 </when> 83 </when>
86 </conditional> 84 </conditional>
87 85
88 <conditional name="OptionXMax"> 86 <conditional name="OptionXMax">
89 <param name="xMax" type="select" label="maximum x-value to plot"> 87 <param name="xMax" type="select" label="maximum value on the x-axis to plot [format: int]">
90 <option value="Yes">Yes</option> 88 <option value="Yes">Yes</option>
91 <option value="No" selected="true">No</option> 89 <option value="No" selected="true">No</option>
92 </param> 90 </param>
93 <when value="Yes"> 91 <when value="Yes">
94 <param name="maxValue" type="integer" value="1000"/> 92 <param name="maxValue" type="integer" value="1000"/>
119 </when> 117 </when>
120 <when value="No"> 118 <when value="No">
121 </when> 119 </when>
122 </conditional> 120 </conditional>
123 121
122
123
124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/> 124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
125
126 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
125 </inputs> 127 </inputs>
126 128
127 <outputs> 129 <outputs>
128 <data name="outputFile" format="png" label="[get sizes] output file"/> 130 <data name="outputFile" format="png" label="[Get sizes] output file"/>
131 <data name="excelOutput" format="csv">
132 <filter>excel</filter>
133 </data>
129 </outputs> 134 </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> 135 </tool>