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comparison data_manager/data_manager_snpEff_databases.xml @ 3:821c34cdacb6 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 17:53:54 -0400
parents c54b7693456f
children a9cace1ee2b7
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2:c54b7693456f 3:821c34cdacb6
1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.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 <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 '$__tool_directory__/data_manager_snpEff_databases.py' 11 data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
12 --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar' 12 </command>
13 '$out_file' 13 <inputs>
14 ]]> 14 </inputs>
15 </command> 15 <outputs>
16 <inputs>
17 </inputs>
18 <outputs>
19 <data name="out_file" format="data_manager_json"/> 16 <data name="out_file" format="data_manager_json"/>
20 </outputs> 17 </outputs>
21 <tests> 18 <tests>
22 <test> 19 <test>
23 <output name="out_file"> 20 <output name="out_file">
24 <assert_contents> 21 <assert_contents>
25 <!-- Check that a genome was added --> 22 <!-- Check that a genome was added -->
26 <has_text text="GRCh38.76" /> 23 <has_text text="GRCh38.76" />
27 </assert_contents> 24 </assert_contents>
28 </output> 25 </output>
29 </test> 26 </test>
30 </tests> 27 </tests>
31 <help> 28 <help>
32 29
33 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. 30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
34 It should only need to be run once for a snpEff version, 31 It should only need to be run once for a snpEff version,
35 since it populates the SnpEff Download data manager from the snpEff config file. 32 since it populates the SnpEff Download data manager from the snpEff config file.
36 33
37 For information about snpEff: http://snpEff.sourceforge.net 34 For information about snpEff: http://snpEff.sourceforge.net
38 35
39 Please cite: 36 Please cite:
40 "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]
41 38
42 </help> 39 </help>
43 <expand macro="citations" /> 40 <citations>
41 <citation type="doi">10.4161/fly.19695</citation>
42 </citations>
44 </tool> 43 </tool>
45 44