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 922b52cf9b35
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922b52cf9b35 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b4991fb40364a975d0ea782035b930874c57665c
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1 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@">
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2 <description>Fixes chimeric alignments from STAR</description>
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3 <macros>
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4 <import>macros.xml</import>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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 fix
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12 '${star_discordant_alignment}'
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13 '${alignment_fixed}'
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14 ]]></command>
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16 <inputs>
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17 <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
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18 </inputs>
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20 <outputs>
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21 <data name="alignment_fixed" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
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22 </outputs>
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24 <tests>
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25 <test>
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26 <param name="star_discordant_alignment" value="fix_test-01.bam"/>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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28 <output name="alignment_fixed" file="fix_test-01.fixed.bam" />
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29 </test>
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30 </tests>
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32 <help><![CDATA[
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34 **What it does**
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36 * Step 1 in dr-disco pipeline
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
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3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
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38 Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers by modifying certain SAM flags and tags.
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
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40 **Attribution**
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42 This work is part of Youri Hoogstrate's PhD thesis.
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44 ]]></help>
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45 <expand macro="citations"/>
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46 </tool>