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comparison dr-disco_integrate.xml @ 3:5348cfd3ba5c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
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children 76a3992021c1
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2:173ca9768e22 3:5348cfd3ba5c
1 <tool id="dr_disco_integrate" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
2 <description>Merges corresponding genomic breaks and exon-to-exon junctions</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements"/>
8 <expand macro="version_command"/>
9
10 <command detect_errors="exit_code"><![CDATA[
11 dr-disco
12 integrate
13 #if $gtf:
14 --gtf ${gtf}
15 #end if
16
17 '${dr_disco_classify_output}'
18 '${dr_disco_integrate_output}'
19 ]]></command>
20
21 <inputs>
22 <param name="dr_disco_classify_output" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
23 <param argument="--gtf" type="data" format="gtf" optional="True" label="GTF file (Optional: for predicting frame shifts)" help="This GTF file requires the following attributes annotated: gene_name, transcript_id and transcript_version"/>
24 </inputs>
25
26 <outputs>
27 <data name="dr_disco_integrate_output" format="tabular" label="${tool.name} on ${dr_disco_classify_output.name}" />
28 </outputs>
29
30 <tests>
31 <test>
32 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
33 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
34
35 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.txt" />
36 </test>
37 <test>
38 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
39 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
40
41 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.no-gtf.txt" />
42 </test>
43 </tests>
44
45 <help><![CDATA[
46
47 **What it does**
48
49
50 **Attributions**
51
52 This work is part of Youri Hoogstrate's PhD thesis.
53
54 ]]></help>
55
56 <expand macro="citations"/>
57 </tool>