Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_integrate.xml @ 4:3de621c44cf9 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 272a4e52b9b11adee8d681a2e84802e945d1112a
author erasmus-medical-center
date Thu, 14 Sep 2017 04:30:12 -0400
parents 5348cfd3ba5c
children 76a3992021c1
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1 <tool id="dr_disco_integrate" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
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2 <description>Merges corresponding genomic breaks and exon-to-exon junctions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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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
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11 dr-disco
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12 integrate
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13 #if $gtf:
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14 --gtf ${gtf}
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15 #end if
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17 '${dr_disco_classify_output}'
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18 '${dr_disco_integrate_output}'
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19 ]]></command>
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21 <inputs>
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22 <param name="dr_disco_classify_output" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
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23 <param argument="--gtf" type="data" format="gtf" optional="True" label="GTF file (Optional: for predicting frame shifts)" help="This GTF file requires the following attributes annotated: gene_name, transcript_id and transcript_version"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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24 </inputs>
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26 <outputs>
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27 <data name="dr_disco_integrate_output" format="tabular" label="${tool.name} on ${dr_disco_classify_output.name}" />
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28 </outputs>
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30 <tests>
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31 <test>
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32 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
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33 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
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35 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.txt" />
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36 </test>
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37 <test>
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38 <param name="dr_disco_classify_output" value="integrate_test_terg_s041.in.dbed" />
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39 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
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41 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.no-gtf.txt" />
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42 </test>
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43 </tests>
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45 <help><![CDATA[
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5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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47 **What it does**
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50 **Attributions**
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5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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52 This work is part of Youri Hoogstrate's PhD thesis.
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54 ]]></help>
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56 <expand macro="citations"/>
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57 </tool>