comparison mergeMutationDatasets.xml @ 56:2a240b005731

better instructions on browser
author jingchunzhu
date Fri, 18 Sep 2015 11:03:59 -0700
parents bb8963939d6f
children
comparison
equal deleted inserted replaced
55:1093078e7976 56:2a240b005731
22 <data name="errorLog" format="data" label="Execution Log" hidden="True" /> 22 <data name="errorLog" format="data" label="Execution Log" hidden="True" />
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***
28 27
29 Output Mutation by Position datafile is ready to be imported into a Xena Hub. 28 **Merge Xena Positional Mutation Datasets**
30 29
31 Output Data Source is of format Rows (Samples) by Columns (identifiers), ready to be imported into a Xena Hub. 30 1. Input xena positional mutation data file format: tab-deliminated
32 31
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. 32 ======= ===== ======= ===== ========= ====== ========
33 sample chr start end reference alt anything
34 ======= ===== ======= ===== ========= ====== ========
35 sample1 chr1 1 1 A T 0.2
36 sample1 chr1 10 10 T A 0.1
37 sample2 chr1 20 20 G GG 0.0
38 sample2 chr1 20 21 GT G
39 ... ... ... ... ... ... ...
40 ======= ===== ======= ===== ========= ====== ========
34 41
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> 42
43 2. Output file 1: Given two datasets of mutation data, 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.
44
45 3. Output file 2: To maintain provenance, this script also outputs a second data file, 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. Users can specify descriptive labels to indicate the data source. </help>
36 </tool> 46 </tool>