comparison dr-disco_fix.xml @ 1:9495360713d4 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
author erasmus-medical-center
date Thu, 16 Mar 2017 04:24:23 -0400
parents fca9c1ace23c
children 173ca9768e22
comparison
equal deleted inserted replaced
0:fca9c1ace23c 1:9495360713d4
1 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0"> 1 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
2 <description>Fixes and annotates chimeric alignments</description> 2 <description>Fixes chimeric alignments from STAR</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 9
10 <command><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 dr-disco fix '${output}' '${star_discordant_alignment}' 11 dr-disco fix '${alignment_fixed}' '${star_discordant_alignment}'
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
14 <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" /> 14 <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
15 </inputs> 15 </inputs>
16 <outputs> 16 <outputs>
17 <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" /> 17 <data name="alignment_fixed" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
18 </outputs> 18 </outputs>
19
19 <tests> 20 <tests>
21 <test>
22 <param name="star_discordant_alignment" value="fix_test-01.bam"/>
23
24 <output name="alignment_fixed" file="fix_test-01.fixed.bam" />
25 </test>
20 </tests> 26 </tests>
21 27
22 <help> 28 <help><![CDATA[
23 </help> 29
24 30 **What it does**
31
32 Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (extract) and for visualization in genome browsers.
33
34 ]]></help>
25 <expand macro="citations"/> 35 <expand macro="citations"/>
26 </tool> 36 </tool>