Mercurial > repos > erasmus-medical-center > dr_disco
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 |
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date | Thu, 16 Mar 2017 04:24:23 -0400 |
parents | fca9c1ace23c |
children | 173ca9768e22 |
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0:fca9c1ace23c | 1:9495360713d4 |
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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> |