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comparison dexseq_count.xml @ 3:a26a82bed63f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
author iuc
date Fri, 25 Sep 2015 16:26:39 -0400
parents 276833129f97
children 28a2181df3b9
comparison
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2:b19cb9385f28 3:a26a82bed63f
1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0"> 1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
2 <description>Prepare and count exon abundancies from RNA-seq data</description> 2 <description>Prepare and count exon abundancies from RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.1.0">R</requirement> 4 <requirement type="package" version="1.14">dexseq</requirement>
5 <requirement type="package" version="1.14.2">dexseq</requirement>
6 <requirement type="package" version="0.6.1">htseq</requirement> 5 <requirement type="package" version="0.6.1">htseq</requirement>
7 <requirement type="package" version="0.7.6">pysam</requirement> 6 <requirement type="package" version="0.7.7">pysam</requirement>
8 </requirements> 7 </requirements>
8 <stdio>
9 <!-- Anything other than zero is an error -->
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <!-- In case the return code has not been set propery check stderr too -->
13 <regex match="Error:" />
14 <regex match="Exception:" />
15 </stdio>
9 <command> 16 <command>
10 <![CDATA[ 17 <![CDATA[
11 #if $mode.mode_select == "prepare": 18 #if $mode.mode_select == "prepare":
12 python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py 19 python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py
13 -r $mode.aggregate 20 -r $mode.aggregate
24 $mode.bamfile 31 $mode.bamfile
25 $counts_file 32 $counts_file
26 #end if 33 #end if
27 ]]> 34 ]]>
28 </command> 35 </command>
29 <stdio>
30 <!-- Anything other than zero is an error -->
31 <exit_code range="1:" />
32 <exit_code range=":-1" />
33 <!-- In case the return code has not been set propery check stderr too -->
34 <regex match="Error:" />
35 <regex match="Exception:" />
36 </stdio>
37 <inputs> 36 <inputs>
38 <conditional name="mode"> 37 <conditional name="mode">
39 <param name="mode_select" type="select" label="Mode of operation"> 38 <param name="mode_select" type="select" label="Mode of operation">
40 <option value="prepare">Prepare annotation</option> 39 <option value="prepare">Prepare annotation</option>
41 <option value="count">Count reads</option> 40 <option value="count">Count reads</option>
64 </conditional> 63 </conditional>
65 </inputs> 64 </inputs>
66 65
67 <outputs> 66 <outputs>
68 <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> 67 <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
69 <filter>(mode['mode_select'] == 'count')</filter> 68 <filter>mode['mode_select'] == 'count'</filter>
70 </data> 69 </data>
71 <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}"> 70 <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
72 <filter>(mode['mode_select'] == 'prepare')</filter> 71 <filter>mode['mode_select'] == 'prepare'</filter>
73 </data> 72 </data>
74 </outputs> 73 </outputs>
75 74
76 <tests> 75 <tests>
77 <test> 76 <test>