Mercurial > repos > melissacline > ucsc_cancer_utilities

comparison mergeMutationDatasets.xml @ 43:eb5acf81e609

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
improve messages
author jingchunzhu
date Fri, 07 Aug 2015 00:13:13 -0700
parents 03b7b1cf78ce
children bb8963939d6f
comparison
equal deleted inserted replaced
42:03b7b1cf78ce 43:eb5acf81e609
12 --bLabel "${inputB.name}" 12 --bLabel "${inputB.name}"
13 #end if 13 #end if
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/> 16 <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/>
17 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. A)" value="dataset A"/> 17 <param type="text" name="labelForDatasetA" label="Dataset A Label (eg. LGG)" value="A"/>
18 <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/> 18 <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/>
19 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. B)" value="dataset B"/> 19 <param type="text" name="labelForDatasetB" label="Dataset B Label (eg. GBM)" value="B"/>
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="errorLog" format="data" label="Execution Log"/> 22 <data name="errorLog" format="data" label="Execution Log"/>
23 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetA}+${labelForDatasetB}"/> 23 <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetA}+${labelForDatasetB}"/>
24 <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetA}+${labelForDatasetB}"/> 24 <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetA}+${labelForDatasetB}"/>
25 </outputs> 25 </outputs>
26 <help> 26 <help>
27 ***Merge Xena Positional Mutation Datasets*** 27 ***Merge Xena Positional Mutation Datasets***
28 28
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
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. 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.
30 34
31 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> 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>
32 </tool> 36 </tool>