Mercurial > repos > melissacline > ucsc_cancer_utilities

comparison segToMatrix.xml @ 52:3a036a34c362

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better handle of input file
author jingchunzhu
date Thu, 17 Sep 2015 15:00:45 -0700
parents 72dc9215623d
children 59dbe857f5d4
comparison
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51:728eda331f07 52:3a036a34c362
24 <data name="outputMatrix" format="tabular" label="xena copy number matrix" /> 24 <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
25 <data name="outputProbeMap" format="tabular" label="associated probemap"/> 25 <data name="outputProbeMap" format="tabular" label="associated probemap"/>
26 </outputs> 26 </outputs>
27 <help> 27 <help>
28 28
29 **Given a segmented copy number data file, convert it into xena ready matrix file.** 29 **Given a segmented copy number data file, convert it into xena ready matrix file.**
30 30
31 Output File no 1. matrix file 31 1. Input data file format: tab-deliminated
32 32
33 Output File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data) 33 ======= ===== ======= ===== ====== ======
34 sanmple chr start end strand value
35 ======= ===== ======= ===== ====== ======
36 sample1 chr1 1 100 . 0.5
37 sample2 chr1 101 1000 . 1.5
38 sample3 chr1 1000 2000 . -0.5
39 ... ... ... ... ... ...
40 ======= ===== ======= ===== ====== ======
41
42
43 2. Output File no 1. matrix file
44
45 Output File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data)
34 </help> 46 </help>
35 </tool> 47 </tool>
36 48