view mergeMutationDatasets.xml @ 47:23d98125d20c

parse snpEff output

<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">
  <command interpreter="python">
      mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog  $inputA $inputB 
      #if $labelForDatasetA
          --aLabel "${labelForDatasetA}"
      #else
          --aLabel "${inputA.name}"
      #end if
      #if $labelForDatasetB
          --bLabel "${labelForDatasetB}"
      #else
          --bLabel "${inputB.name}"
      #end if
  </command>
  <inputs>
    <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/>
    <param type="text" name="labelForDatasetA"  label="Dataset A Label (eg. LGG)" value="A"/>
    <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/> 
    <param type="text" name="labelForDatasetB"  label="Dataset B Label (eg. GBM)" value="B"/>
 </inputs>
  <outputs>
    <data name="errorLog" format="data" label="Execution Log" hidden="True" />
    <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetA}+${labelForDatasetB}"/> 
    <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetA}+${labelForDatasetB}"/>
  </outputs>
  <help>
    ***Merge Xena Positional Mutation Datasets***

    Output Mutation by Position datafile is ready to be imported into a Xena Hub.

    Output Data Source is of format Rows (Samples) by Columns (identifiers), ready to be imported into a Xena Hub.

    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. 

    To maintain provenance, this script also outputs a second matrix, with one row for each sample ID that appears in the output dataset, and two columns per row indicating which input dataset(s) contained some mutation data for that sample.  By default, the input dataset name is used to indicate which input file each column came from.  Optionally, the user can specify descriptive labels to be used in place of the dataset names.   </help>
</tool>