Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate seg2matrix/segToMatrix.xml @ 31:ab20c0d04f4a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add seg2matrix tool
author jingchunzhu
date Fri, 24 Jul 2015 13:10:11 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
1 <tool id="segToMatrix" name="segToMatrix" version="0.0.1">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
2 <description>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
3 Prep segmented copy number data for Xena
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
4 </description>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
5 <command interpreter="python">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
6 segToMatrixGalaxy.py $input $refGene.assembly $outputMatrix $outputProbeMap
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
7 </command>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
8 <inputs>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
9 <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" />
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
10 <conditional name="refGene">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
11 <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
12 <option value="hg19">hg19</option>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
13 <option value="hg18">hg18</option>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
14 </param>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
15 <when value="hg19">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
16 <param name="assembly" type="hidden" value="refGene_hg19" />
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
17 </when>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
18 <when value="hg18">
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
19 <param name="assembly" type="hidden" value="refGene_hg18" />
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
20 </when>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
21 </conditional>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
22 </inputs>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
23 <outputs>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
24 <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
25 <data name="outputProbeMap" format="tabular" label="associated probemap"/>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
26 </outputs>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
27 <help>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
28 ***Convert segmented copy number data for input into xena***
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
29
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
30 Given a segmented copy number data file, convert it into xena ready data files.
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
31
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
32 File no 1. matrix file
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
33 File no 2. probeMap file -- probe to gene mapping file (is in the same genome assembly as the input segmented copy number data)
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
34 </help>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
35 </tool>
ab20c0d04f4a add seg2matrix tool
jingchunzhu
parents:
diff changeset
36