|
0
|
1 <tool id="soft_threshold" name="wgcna soft threshold" version="1.0.0">
|
|
|
2 <description>
|
|
|
3 Calculate R power table and explore optimal beta value
|
|
|
4 </description>
|
|
|
5 <stdio>
|
|
|
6 <regex match="Execution halted"
|
|
|
7 source="both"
|
|
|
8 level="fatal"
|
|
|
9 description="Execution halted." />
|
|
|
10 <regex match="Error in"
|
|
|
11 source="both"
|
|
|
12 level="fatal"
|
|
|
13 description="An undefined error occured, please check your intput carefully and contact your administrator." />
|
|
|
14 <regex match="Fatal error"
|
|
|
15 source="both"
|
|
|
16 level="fatal"
|
|
|
17 description="An undefined error occured, please check your intput carefully and contact your administrator." />
|
|
|
18 </stdio>
|
|
|
19 <requirements>
|
|
|
20 <requirement type="package" version="3.2.1">R</requirement>
|
|
|
21 <requirement type="package" version="1.0.0">wgcna</requirement>
|
|
|
22 </requirements>
|
|
|
23 <command>
|
|
|
24 <![CDATA[
|
|
|
25 Rscript '${__tool_directory__}/soft_threshold.R'
|
|
|
26 -t $threads
|
|
|
27 -f $expressionData
|
|
|
28 -b $betaMaximum
|
|
|
29 -r $rPowerTable
|
|
|
30 -p $scaleFreeFitPlot
|
|
|
31 ]]>
|
|
|
32 </command>
|
|
|
33 <inputs>
|
|
|
34 <param name="threads" type="integer" value="1" label="number of threads for WGCNA"/>
|
|
|
35 <param name="expressionData" type="data" format="csv" label="expression data in csv file format. Rows are samples and columns are genes"/>
|
|
|
36 <param name="betaMaximum" type="integer" value="12" label="maximum beta values"/>
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="csv" name="rPowerTable" label="R power table on ${on_string}" />
|
|
|
40 <data format="pdf" name="scaleFreeFitPlot" label="scale free fit plot on ${on_string}" />
|
|
|
41 </outputs>
|
|
5
|
42 </tool>
|
