Mercurial > repos > jetbrains > cmeth

annotate cmeth.xml @ 1:5efe658422eb

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Sadly XTransform not supported
author oleg@oleg-desktop.times.labs.intellij.net
date Thu, 29 Oct 2015 16:42:41 +0300
parents d7714f886224
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
1 <tool id="cmeth" name="Cmeth" version="0.2.0">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
2 <description>BS-Seq analysis</description>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
3 <requirements>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
4 <requirement type="package" version="0.0.1">integration_jar</requirement>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
5 </requirements>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
6 <stdio>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
7 <!-- Wrapper ensures anything other than zero is an error -->
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
8 <exit_code range="1:"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
9 <exit_code range=":-1"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
10 </stdio>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
11 <command interpreter="python">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
12 #if $action.selection == "analyze"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
13 cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
14 #else
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
15 cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
16 #end if
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
17 </command>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
18 <inputs>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
19 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
20 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
21 <conditional name="action">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
22 <param name="selection" type="select" label="Action">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
23 <option value="analyze">Compute methylation</option>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
24 <option value="compare">Compare methylation</option>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
25 </param>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
26 <when value="analyze">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
27 <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
28 </when>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
29 <when value="compare">
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
30 <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
31 <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
32 </when>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
33 </conditional>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
34 </inputs>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
35 <outputs>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
36 #if $action.selection == "analyze"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
37 <data name="result" format="csv" label="CG_unmethylated.csv"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
38 #else
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
39 <data name="result" format="csv" label="CG_emr.csv"/>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
40 #end if
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
41 </outputs>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
42 <help>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
43 Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data.
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
44 Both procedures rely on the nonparametric Bayesian switching HMM.
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
45 https://github.com/JetBrains-Research/cmeth
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
46 </help>
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
47 </tool>