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annotate data_manager/data_manager_snpEff_databases.xml @ 2:984733fcab49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 47cd0cc3b680295e6bea84acc89f18c79b6d3f0c
author iuc
date Tue, 07 Jun 2016 15:44:15 -0400
parents 85a23e2dd92b
children e5a471c4630e
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
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2 <description>Read the list of available snpEff databases</description>
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3 <requirements>
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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4 <requirement type="package" version="4.1">snpEff</requirement>
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5 </requirements>
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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6 <stdio>
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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8 <exit_code range="1:" level="fatal" description="Error" />
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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9 </stdio>
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10 <command interpreter="python">
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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11 data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
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12 </command>
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13 <inputs>
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14 </inputs>
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15 <outputs>
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16 <data name="out_file" format="data_manager_json"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <output name="out_file">
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21 <assert_contents>
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22 <!-- Check that a genome was added -->
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23 <has_text text="GRCh38.76" />
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24 </assert_contents>
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25 </output>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
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31 It should only need to be run once for a snpEff version,
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32 since it populates the SnpEff Download data manager from the snpEff config file.
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33
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34 For information about snpEff: http://snpEff.sourceforge.net
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35
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36 Please cite:
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37 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
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39 </help>
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85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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40 <citations>
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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41 <citation type="doi">10.4161/fly.19695</citation>
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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42 </citations>
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43 </tool>
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