Mercurial > repos > jetbrains > zinbra

annotate zinbra.xml @ 1:8cbb06892b62

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Release version: https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5
author Oleg Shpynov <oleg.shpynov@gmail.com>
date Wed, 28 Oct 2015 11:28:49 +0300
parents 5f97f28e65ca
children 0eb50728861a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
1 <tool id="zinbra" name="Zinbra" version="0.0.1">
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
2 <description>ChIP-Seq enrichment</description>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
3 <requirements>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
4 <requirement type="package" version="0.0.1">epigenome</requirement>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
5 </requirements>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
6 <stdio>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
7 <!-- Wrapper ensures anything other than zero is an error -->
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
8 <exit_code range="1:" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
9 <exit_code range=":-1" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
10 </stdio>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
11 <command interpreter="python">
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
12 zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
13 </command>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
14 <inputs>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
15 <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" />
1
8cbb06892b62 Release version:
Oleg Shpynov <oleg.shpynov@gmail.com>
parents: 0
diff changeset
16 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference" />
0
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
17 <param name="bin" size="5" type="integer" value="200" label="Bin size" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
18 <param name="fdr" size="5" type="float" value="0.0001" label="FDR" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
19 </inputs>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
20 <outputs>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
21 <data name="result" format="bed" label="result.bed" />
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
22 </outputs>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
23 <help>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
24 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.
1
8cbb06892b62 Release version:
Oleg Shpynov <oleg.shpynov@gmail.com>
parents: 0
diff changeset
25 https://github.com/JetBrains-Research/zinbra
0
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
26 </help>
5f97f28e65ca Initial commit
Oleg Shpynov <oleg.shpynov@gmail.com>
parents:
diff changeset
27 </tool>