Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_fix.xml @ 0:fca9c1ace23c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
author erasmus-medical-center
date Wed, 25 Jan 2017 08:06:06 -0500
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children 9495360713d4
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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
erasmus-medical-center
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1 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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2 <description>Fixes and annotates chimeric alignments</description>
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>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
erasmus-medical-center
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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" />
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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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10 <command><![CDATA[
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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11 dr-disco fix '${output}' '${star_discordant_alignment}'
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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12 ]]></command>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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13 <inputs>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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14 <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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15 </inputs>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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16 <outputs>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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17 <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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18 </outputs>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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19 <tests>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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20 </tests>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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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22 <help>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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23 </help>
fca9c1ace23c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
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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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25 <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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26 </tool>