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comparison mergeMutationDatasets.xml @ 41:9806198df91f

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fix
author jingchunzhu
date Thu, 06 Aug 2015 00:27:05 -0700
parents 3a259686f0fc
children 03b7b1cf78ce
comparison
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40:72dc9215623d 41:9806198df91f
1 <tool id="mergeMutationDatasets" description="Merge two Xena positional mutation datasets into a new dataset" name="Merge Positional Mutation Data" version="0.0.1"> 1 <tool id="mergeMutationDatasets" description="Merge two Xena positional mutation datasets into a new dataset" name="Merge Xena Mutation by Position Data" version="0.0.1">
2 <description>
3 Given two mutation datasets, merge them to create a larger dataset with the mutations from both datasets. Output this larger dataset, along with a 2-column matrix indicating the source of each mutation
4 </description>
5 <command interpreter="python"> 2 <command interpreter="python">
6 mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog $inputA $inputB 3 mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog $inputA $inputB
7 #if $labelForDatasetA 4 #if $labelForDatasetA
8 --aLabel "${labelForDatasetA}" 5 --aLabel "${labelForDatasetA}"
6 #else
7 --aLabel "${inputA.name}"
9 #end if 8 #end if
10 #if $labelForDatasetB 9 #if $labelForDatasetB
11 --bLabel "${labelForDatasetB}" 10 --bLabel "${labelForDatasetB}"
11 #else
12 --bLabel "${inputB.name}"
12 #end if 13 #end if
13 </command> 14 </command>
14 <inputs> 15 <inputs>
15 <param name="inputA" format="tabular" type="data" label="Mutation Dataset A"/> 16 <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/>
16 <param type="text" name="labelForDatasetA" label="Dataset A Label (optional)" optional="true"/> 17 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. A)" value="dataset A"/>
17 <param name="inputB" format="tabular" type="data" label="Mutation Dataset B"/> 18 <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/>
18 <param type="text" name="labelForDatasetB" label="Dataset B Label (optional)" optional="true"/> 19 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. B)" value="dataset B"/>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data name="errorLog" format="data" label="Execution Log"/> 22 <data name="errorLog" format="data" label="Execution Log"/>
22 <data name="outputSourceMatrix" format="tabular" label="Mutation Data Sources"/> 23 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetB}+${labelForDatasetA}"/>
23 <data name="outputC" format="tabular" label="Merged Mutation Data"/> 24 <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetB}+${labelForDatasetA}"/>
24 </outputs> 25 </outputs>
25 <help> 26 <help>
26 ***Merge Xena Positional Mutation Datasets*** 27 ***Merge Xena Positional Mutation Datasets***
27 28
28 Given two datasets of mutation data as formatted for the UCSC Xena Browser, merge them to produce a third dataset that is the union of the first two. The new dataset will contain all mutations from either dataset. 29 Given two datasets of mutation data as formatted for the UCSC Xena Browser, merge them to produce a third dataset that is the union of the first two. The new dataset will contain all mutations from either dataset.