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comparison data_manager/data_manager_snpEff_databases.xml @ 1:85a23e2dd92b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
author iuc
date Tue, 07 Jun 2016 10:11:50 -0400
parents 9ac823a8b328
children e5a471c4630e
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0:9ac823a8b328 1:85a23e2dd92b
1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.0.0" tool_type="manage_data"> 1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
2 <description>Read the list of available snpEff databases</description> 2 <description>Read the list of available snpEff databases</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.0">snpEff</requirement> 4 <requirement type="package" version="4.1">snpEff</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio>
6 <command interpreter="python"> 10 <command interpreter="python">
7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file" 11 data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
8 </command> 12 </command>
9 <inputs> 13 <inputs>
10 </inputs> 14 </inputs>
11 <outputs> 15 <outputs>
12 <data name="out_file" format="data_manager_json"/> 16 <data name="out_file" format="data_manager_json"/>
13 </outputs> 17 </outputs>
14 <stdio>
15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
16 <exit_code range="1:" level="fatal" description="Error" />
17 </stdio>
18 <tests> 18 <tests>
19 <test> 19 <test>
20 <output name="out_file"> 20 <output name="out_file">
21 <assert_contents> 21 <assert_contents>
22 <!-- Check that a genome was added --> 22 <!-- Check that a genome was added -->
35 35
36 Please cite: 36 Please cite:
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] 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]
38 38
39 </help> 39 </help>
40 <citations>
41 <citation type="doi">10.4161/fly.19695</citation>
42 </citations>
40 </tool> 43 </tool>
41 44