Mercurial > repos > erasmus-medical-center > dr_disco

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
author erasmus-medical-center
date Fri, 03 Nov 2017 07:23:57 -0400
parents f2c70d589596
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1 <tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@">
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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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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
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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="tabular" 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: gene_name, transcript_id and transcript_version"/>
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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 <!--
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40 <param name="gtf" value="integrate_tmprss-erg.hg38.gtf" />
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41 -->
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43 <output name="dr_disco_integrate_output" file="integrate_test_terg_s041.out.no-gtf.txt" />
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44 </test>
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45 </tests>
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47 <help><![CDATA[
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49 **What it does**
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51 * Step 4 in dr-disco pipeline
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53 In this step the predicted junctions are integrated with a gene annotation. The junctions are provided names like 'TMPRSS2->ERG' and frameshift are provided. Also events that belong to each other, thus the intronic and exonic junctions that belong to the same genomic event, are given the same identifier.
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55 **Attribution**
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57 This work is part of Youri Hoogstrate's PhD thesis.
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59 ]]></help>
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61 <expand macro="citations"/>
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62 </tool>