Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_fix.xml @ 3:5348cfd3ba5c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
parents 173ca9768e22
children 922b52cf9b35
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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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1 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
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2 <description>Fixes chimeric alignments from STAR</description>
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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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7 <expand macro="requirements" />
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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8 <expand macro="version_command" />
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10 <command detect_errors="exit_code"><![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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11 dr-disco fix
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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12 '${star_discordant_alignment}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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13 '${alignment_fixed}'
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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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14 ]]></command>
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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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16 <inputs>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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17 <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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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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" />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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29 </test>
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30 </tests>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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32 <help><![CDATA[
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34 **What it does**
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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36 Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers.
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38 ]]></help>
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39 <expand macro="citations"/>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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40 </tool>