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comparison data_manager/data_manager_snpEff_download.xml @ 4:847b0f43c0e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:14:37 -0400
parents e5a471c4630e
children 3d9dd4b9fb09
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3:e5a471c4630e 4:847b0f43c0e5
1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data"> 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
2 <description>Download a new database</description> 2 <description>Download a new database</description>
3 <macros> 3 <requirements>
4 <import>snpEff_macros.xml</import> 4 <requirement type="package" version="4.1">snpEff</requirement>
5 </macros> 5 </requirements>
6 <expand macro="requirements" /> 6 <stdio>
7 <expand macro="stdio" /> 7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <expand macro="version_command" /> 8 <exit_code range="1:" level="fatal" description="Error" />
9 <command><![CDATA[ 9 </stdio>
10 @CONDA_SNPEFF_JAR_PATH@ && 10 <command interpreter="python">
11 python $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config" 11 data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
12 --genome_version "$genome_version" "$out_file" 12 --genome_version "$genome_version" "$out_file"
13 ]]> 13 </command>
14 </command>
15 <inputs> 14 <inputs>
16 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 15 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
17 <help>https://snpeff-data.galaxyproject.org/databases/</help> 16 <help>https://snpeff-data.galaxyproject.org/databases/</help>
18 <validator type="regex" message="A genome version name is required">\S+</validator> 17 <validator type="regex" message="A genome version name is required">\S+</validator>
19 </param> 18 </param>
48 47
49 Please cite: 48 Please cite:
50 "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] 49 "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]
51 50
52 </help> 51 </help>
53 <expand macro="citations" /> 52 <citations>
53 <citation type="doi">10.4161/fly.19695</citation>
54 </citations>
54 </tool> 55 </tool>
55 56