Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_detect.xml @ 2:173ca9768e22 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
author erasmus-medical-center
date Fri, 28 Apr 2017 03:56:08 -0400
parents 9495360713d4
children 5348cfd3ba5c
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1 <tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
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2 <description>Detects break-points in RNA-seq</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 detect
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13 --min-e-score '${min_e_score}'
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14 '${table_fusion_events}'
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15 '${star_discordant_alignment_fixed}'
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16 ]]></command>
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17 <inputs>
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18 <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
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19 <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0"
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20 label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
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21 </inputs>
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23 <outputs>
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24 <data name="table_fusion_events" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" />
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25 </outputs>
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27 <tests>
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28 <test>
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29 <param name="star_discordant_alignment_fixed" value="detect.bam" />
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30 <param name="min_e_score" value="8" />
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32 <output name="table_fusion_events" file="detect.txt" />
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33 </test>
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34 </tests>
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36 <help><![CDATA[
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38 **What it does**
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40 Detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure.
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42 This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads.
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44 **Attributions**
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46 This work is part of Youri Hoogstrate's PhD thesis.
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1
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48 ]]></help>
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50 <expand macro="citations"/>
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51 </tool>