Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate segToMatrix.xml @ 54:59dbe857f5d4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
introduce normal_CNV parameter
author jingchunzhu
date Thu, 17 Sep 2015 22:03:04 -0700
parents 3a036a34c362
children 2a240b005731
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
1 <tool id="segToMatrix" name="segToMatrix" version="0.0.1">
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
2 <description>
40
72dc9215623d modify help
jingchunzhu
parents: 39
diff changeset
3 Prepare segmented copy number data for Xena
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
4 </description>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
5 <command interpreter="python">
54
59dbe857f5d4 introduce normal_CNV parameter
jingchunzhu
parents: 52
diff changeset
6 seg2matrix/segToMatrixGalaxy.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap $normal_CNV_value
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
7 </command>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
8 <inputs>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" />
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
10 <conditional name="refGene">
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?">
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
12 <option value="hg19">hg19</option>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
13 <option value="hg18">hg18</option>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
14 </param>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
15 <when value="hg19">
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
16 <param name="assembly" type="hidden" value="refGene_hg19" />
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
17 </when>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
18 <when value="hg18">
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
19 <param name="assembly" type="hidden" value="refGene_hg18" />
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
20 </when>
54
59dbe857f5d4 introduce normal_CNV parameter
jingchunzhu
parents: 52
diff changeset
21 </conditional>
59dbe857f5d4 introduce normal_CNV parameter
jingchunzhu
parents: 52
diff changeset
22 <param name="normal_CNV_value" type="text" value="0" lable="what is the value to represent normal copy number" />
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
23 </inputs>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
24 <outputs>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
25 <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
26 <data name="outputProbeMap" format="tabular" label="associated probemap"/>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
27 </outputs>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
28 <help>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
29
52
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
30 **Given a segmented copy number data file, convert it into xena ready matrix file.**
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
31
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
32 1. Input data file format: tab-deliminated
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
33
52
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
34 ======= ===== ======= ===== ====== ======
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
35 sanmple chr start end strand value
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
36 ======= ===== ======= ===== ====== ======
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
37 sample1 chr1 1 100 . 0.5
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
38 sample2 chr1 101 1000 . 1.5
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
39 sample3 chr1 1000 2000 . -0.5
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
40 ... ... ... ... ... ...
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
41 ======= ===== ======= ===== ====== ======
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
42
52
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
43
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
44 2. Output File no 1. matrix file
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
45
3a036a34c362 better handle of input file
jingchunzhu
parents: 40
diff changeset
46 Output File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data)
32
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
47 </help>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
48 </tool>
8e888e966c47 change segToMatrix.xml location
jingchunzhu
parents:
diff changeset
49