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comparison segToGeneMatrix.xml @ 51:728eda331f07

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better handle of input
author jingchunzhu@gmail.com
date Thu, 17 Sep 2015 14:33:21 -0700
parents 72dc9215623d
children 59dbe857f5d4
comparison
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50:b6f5d2d1b047 51:728eda331f07
4 </description> 4 </description>
5 <command interpreter="python"> 5 <command interpreter="python">
6 seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix 6 seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix
7 </command> 7 </command>
8 <inputs> 8 <inputs>
9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" /> 9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" help="See input data format section for required input format" />
10 <conditional name="refGene"> 10 <conditional name="refGene">
11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?"> 11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?" help="Copy number segments will be map to RefGenes of the selected assembly.">
12 <option value="hg19">hg19</option> 12 <option value="hg19">hg19</option>
13 <option value="hg18">hg18</option> 13 <option value="hg18">hg18</option>
14 </param> 14 </param>
15 <when value="hg19"> 15 <when value="hg19">
16 <param name="assembly" type="hidden" value="refGene_hg19" /> 16 <param name="assembly" type="hidden" value="refGene_hg19" />
23 <outputs> 23 <outputs>
24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" /> 24 <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" />
25 </outputs> 25 </outputs>
26 <help> 26 <help>
27 27
28 **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready** 28 **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready**
29 29
30 Output File no 1. matrix file 30 1. Input data file format: tab-deliminated
31
32 ======= ===== ======= ===== ====== ======
33 sanmple chr start end strand value
34 ======= ===== ======= ===== ====== ======
35 sample1 chr1 1 100 . 0.5
36 sample2 chr1 101 1000 . 1.5
37 sample3 chr1 1000 2000 . -0.5
38 ... ... ... ... ... ...
39 ======= ===== ======= ===== ====== ======
40
41
42 2. Output file: gene-level matrix file
31 43
32 </help> 44 </help>
33 </tool> 45 </tool>
34 46