diff mergeGenomicFiles.xml @ 14:d0b8c8eee9d5

Committing changes that hadn't made it in yet, merge hell

--- a/mergeGenomicFiles.xml	Tue Mar 10 19:29:10 2015 -0700
+++ b/mergeGenomicFiles.xml	Tue Mar 10 19:32:14 2015 -0700
@@ -1,20 +1,31 @@
 <tool id="mergeGenomicFiles" description="Merge two genomic datasets into a new dataset" name="mergeGenomicFiles" version="0.0.1">
   <description>
-    Given two genomic datasets, merge them to create a third dataset with the row and column identifiers from both datasets.
+    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
   </description>
   <command interpreter="python">
-      mergeGenomicMatrixFiles.py $outputC $inputA $inputB
+      mergeGenomicMatrixFiles.py $inputA $inputB $outputC $outputSourceMatrix
+      #if $labelForDatasetA
+          --aLabel "${labelForDatasetA}"
+      #end if
+      #if $labelForDatasetB
+          --bLabel "${labelForDatasetB}"
+      #end if
   </command>
   <inputs>
     <param name="inputA" format="tabular" type="data" label="Genomic Dataset A"/>
-    <param name="inputB" format="tabular" type="data" label="Genomic Dataset B"/>
-  </inputs>
+    <param type="text" name="labelForDatasetA"  label="Dataset A Label (optional)" optional="true"/>
+    <param name="inputB" format="tabular" type="data" label="Genomic Dataset B"/> 
+    <param type="text" name="labelForDatasetB"  label="Dataset B Label (optional)" optional="true"/>
+ </inputs>
   <outputs>
     <data name="outputC" format="tabular"/>
+    <data name="outputSourceMatrix" format="tabular"/>
   </outputs>
   <help>
     ***Merge Genomic Datasets***
 
-    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 da
+    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.
+
+    To maintain provenance, this script also outputs a second matrix, with one row for each column in the output dataset, and two columns per row indicating which input dataset that column came from.  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 filenames.  This all assumes that each column exists in only one input dataset.
   </help>
 </tool>