Mercurial > repos > melissacline > ucsc_cancer_utilities
annotate mergeMutationDatasets.xml @ 52:3a036a34c362
better handle of input file
| author | jingchunzhu |
|---|---|
| date | Thu, 17 Sep 2015 15:00:45 -0700 |
| parents | bb8963939d6f |
| children | 2a240b005731 |
| rev | line source |
|---|---|
| 41 | 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"> |
| 19 | 2 <command interpreter="python"> |
| 3 mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog $inputA $inputB | |
| 4 #if $labelForDatasetA | |
| 5 --aLabel "${labelForDatasetA}" | |
| 41 | 6 #else |
| 7 --aLabel "${inputA.name}" | |
| 19 | 8 #end if |
| 9 #if $labelForDatasetB | |
| 10 --bLabel "${labelForDatasetB}" | |
| 41 | 11 #else |
| 12 --bLabel "${inputB.name}" | |
| 19 | 13 #end if |
| 14 </command> | |
| 15 <inputs> | |
| 41 | 16 <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/> |
| 43 | 17 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. LGG)" value="A"/> |
| 41 | 18 <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/> |
| 43 | 19 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. GBM)" value="B"/> |
| 19 | 20 </inputs> |
| 21 <outputs> | |
| 44 | 22 <data name="errorLog" format="data" label="Execution Log" hidden="True" /> |
| 42 | 23 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetA}+${labelForDatasetB}"/> |
| 24 <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetA}+${labelForDatasetB}"/> | |
| 19 | 25 </outputs> |
| 26 <help> | |
|
21
3a259686f0fc
Merged with head, tweaked labels on merge mutation data tool
melissacline
parents:
20
diff
changeset
|
27 ***Merge Xena Positional Mutation Datasets*** |
| 19 | 28 |
| 43 | 29 Output Mutation by Position datafile is ready to be imported into a Xena Hub. |
| 30 | |
| 31 Output Data Source is of format Rows (Samples) by Columns (identifiers), ready to be imported into a Xena Hub. | |
| 32 | |
| 19 | 33 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. |
| 34 | |
| 35 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> | |
| 36 </tool> |