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comparison mergeGenomicFiles.xml @ 41:9806198df91f

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fix
author jingchunzhu
date Thu, 06 Aug 2015 00:27:05 -0700
parents 3a259686f0fc
children 03b7b1cf78ce
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40:72dc9215623d 41:9806198df91f
1 <tool id="mergeGenomicFiles" description="Merge two genomic datasets into a new dataset" name="Merge Genomic Datasets" version="0.0.1"> 1 <tool id="mergeGenomicFiles" description="Merge two genomic matrices into a new dataset" name="Merge Genomic Matrix Datasets" version="0.0.1">
2 <description> 2 <description>
3 Given two genomic datasets, merge them to create a larger dataset with the row and column identifiers from both datasets. Output this larger dataset, along with a 2-column matrix indicating the source file of each sample 3 Given two genomic datasets, merge them to create a larger dataset with the row and column identifiers from both datasets. Output this larger dataset, along with a 2-column matrix indicating the source file of each sample
4 </description> 4 </description>
5 <command interpreter="python"> 5 <command interpreter="python">
6 mergeGenomicMatrixFiles.py $inputA $inputB $outputC $outputSourceMatrix 6 mergeGenomicMatrixFiles.py $inputA $inputB $outputC $outputSourceMatrix
7 #if $labelForDatasetA 7 #if $labelForDatasetA
8 --aLabel "${labelForDatasetA}" 8 --aLabel "${labelForDatasetA}"
9 #else
10 --aLabel "${inputA.name}"
9 #end if 11 #end if
10 #if $labelForDatasetB 12 #if $labelForDatasetB
11 --bLabel "${labelForDatasetB}" 13 --bLabel "${labelForDatasetB}"
14 #else
15 --bLabel "${inputB.name}"
12 #end if 16 #end if
13 </command> 17 </command>
14 <inputs> 18 <inputs>
15 <param name="inputA" format="tabular" type="data" label="Genomic Dataset A"/> 19 <param name="inputA" format="tabular" type="data" label="Genomic Matrix A"/>
16 <param type="text" name="labelForDatasetA" label="Dataset A Label (optional)" optional="true"/> 20 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. A)" value="dataset A"/>
17 <param name="inputB" format="tabular" type="data" label="Genomic Dataset B"/> 21 <param name="inputB" format="tabular" type="data" label="Genomic Matrix B"/>
18 <param type="text" name="labelForDatasetB" label="Dataset B Label (optional)" optional="true"/> 22 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. B)" value="dataset B"/>
19 </inputs> 23 </inputs>
20 <outputs> 24 <outputs>
21 <data name="outputSourceMatrix" format="tabular" label="Genomic Data Sources"/> 25 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetB}+${labelForDatasetA}"/>
22 <data name="outputC" format="tabular" label="Merged Genomic Data"/> 26 <data name="outputC" format="tabular" label="Genomic Matrix ${labelForDatasetB}+${labelForDatasetA}"/>
23 </outputs> 27 </outputs>
24 <help> 28 <help>
25 ***Merge Genomic Datasets*** 29 ***Merge Genomic Datasets***
26 30
27 Given two genomic datasets, merge them to produce a third dataset that is the union of the first two. The new dataset will contain all column labels from either dataset, and all row labels from either dataset. If a row label appears in both datasets, the output dataset will contain, for that row, all values for the first set of columns, plus all values for the second set of columns. If a row label appears in the first dataset only, the output dataset will contain the values for the columns of the first dataset, and blanks (indicating missing values) for the columns of the second dataset. 31 Given two genomic datasets, merge them to produce a third dataset that is the union of the first two. The new dataset will contain all column labels from either dataset, and all row labels from either dataset. If a row label appears in both datasets, the output dataset will contain, for that row, all values for the first set of columns, plus all values for the second set of columns. If a row label appears in the first dataset only, the output dataset will contain the values for the columns of the first dataset, and blanks (indicating missing values) for the columns of the second dataset.