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comparison data_manager/data_manager_snpEff_download.xml @ 3:e5a471c4630e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:13:11 -0400
parents 85a23e2dd92b
children 847b0f43c0e5
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2:984733fcab49 3:e5a471c4630e
1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data"> 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
2 <description>Download a new database</description> 2 <description>Download a new database</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="4.1">snpEff</requirement> 4 <import>snpEff_macros.xml</import>
5 </requirements> 5 </macros>
6 <stdio> 6 <expand macro="requirements" />
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 7 <expand macro="stdio" />
8 <exit_code range="1:" level="fatal" description="Error" /> 8 <expand macro="version_command" />
9 </stdio> 9 <command><![CDATA[
10 <command interpreter="python"> 10 @CONDA_SNPEFF_JAR_PATH@ &&
11 data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config" 11 python $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
12 --genome_version "$genome_version" "$out_file" 12 --genome_version "$genome_version" "$out_file"
13 </command> 13 ]]>
14 </command>
14 <inputs> 15 <inputs>
15 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 16 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
16 <help>https://snpeff-data.galaxyproject.org/databases/</help> 17 <help>https://snpeff-data.galaxyproject.org/databases/</help>
17 <validator type="regex" message="A genome version name is required">\S+</validator> 18 <validator type="regex" message="A genome version name is required">\S+</validator>
18 </param> 19 </param>
47 48
48 Please cite: 49 Please cite:
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] 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]
50 51
51 </help> 52 </help>
52 <citations> 53 <expand macro="citations" />
53 <citation type="doi">10.4161/fly.19695</citation>
54 </citations>
55 </tool> 54 </tool>
56 55