Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/getSizes.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
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14:c79b9ae3f65f 15:440ceca58672
19 #end if 19 #end if
20 #if $OptionY.yLab == "Yes": 20 #if $OptionY.yLab == "Yes":
21 -b $OptionY.yLabValue 21 -b $OptionY.yLabValue
22 #end if 22 #end if
23 $barPlot 23 $barPlot
24 $excel $excelOutput
25 </command> 24 </command>
26 25
27 <inputs> 26 <inputs>
28 <conditional name="formatType"> 27 <conditional name="formatType">
29 <param name="FormatInputFileName" type="select" label="Input File Format"> 28 <param name="FormatInputFileName" type="select" label="Input File Format">
82 81
83 </when> 82 </when>
84 </conditional> 83 </conditional>
85 84
86 <conditional name="OptionXMax"> 85 <conditional name="OptionXMax">
87 <param name="xMax" type="select" label="maximum value on the x-axis to plot [format: int]"> 86 <param name="xMax" type="select" label="maximum x-value to plot">
88 <option value="Yes">Yes</option> 87 <option value="Yes">Yes</option>
89 <option value="No" selected="true">No</option> 88 <option value="No" selected="true">No</option>
90 </param> 89 </param>
91 <when value="Yes"> 90 <when value="Yes">
92 <param name="maxValue" type="integer" value="1000"/> 91 <param name="maxValue" type="integer" value="1000"/>
117 </when> 116 </when>
118 <when value="No"> 117 <when value="No">
119 </when> 118 </when>
120 </conditional> 119 </conditional>
121 120
122
123
124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/> 121 <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."/>
127 </inputs> 122 </inputs>
128 123
129 <outputs> 124 <outputs>
130 <data name="outputFile" format="png" label="[Get size] Output file"/> 125 <data name="outputFile" format="png" label="[Get sizes] output file"/>
131 <data name="excelOutput" format="csv">
132 <filter>excel</filter>
133 </data>
134 </outputs> 126 </outputs>
127
128 <help>
129 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
130
131 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.
132 </help>
135 </tool> 133 </tool>