Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_integrate.xml @ 5:76a3992021c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit f6f9296f2774ba81f81f57d5f80d597d008e6a1c
author erasmus-medical-center
date Thu, 14 Sep 2017 05:09:34 -0400
parents 5348cfd3ba5c
children 6b87499054f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
76a3992021c1 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit f6f9296f2774ba81f81f57d5f80d597d008e6a1c
erasmus-medical-center
parents: 3
diff changeset
1 <tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@-g0">
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
2 <description>Merges corresponding genomic breaks and exon-to-exon junctions</description>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
3 <macros>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
4 <import>macros.xml</import>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
5 </macros>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
6
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
7 <expand macro="requirements"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
8 <expand macro="version_command"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
9
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
11 dr-disco
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
12 integrate
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
13 #if $gtf:
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
14 --gtf ${gtf}
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
15 #end if
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
16
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
17 '${dr_disco_classify_output}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
18 '${dr_disco_integrate_output}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
19 ]]></command>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
20
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
21 <inputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
22 <param name="dr_disco_classify_output" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
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"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
24 </inputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
25
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
26 <outputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
27 <data name="dr_disco_integrate_output" format="tabular" label="${tool.name} on ${dr_disco_classify_output.name}" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
28 </outputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
29
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
30 <tests>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
31 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
32 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
33 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
34
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
35 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.txt" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
36 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
37 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
38 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
39 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
40
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
41 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.no-gtf.txt" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
42 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
43 </tests>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
44
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
45 <help><![CDATA[
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
46
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
47 **What it does**
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
48
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
49
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
50 **Attributions**
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
51
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
52 This work is part of Youri Hoogstrate's PhD thesis.
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
53
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
54 ]]></help>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
55
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
56 <expand macro="citations"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
57 </tool>