Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_databases.xml @ 3:e5a471c4630e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author | iuc |
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date | Mon, 31 Oct 2016 08:13:11 -0400 |
parents | 85a23e2dd92b |
children | 847b0f43c0e5 |
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2:984733fcab49 | 3:e5a471c4630e |
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data"> | 1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.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 <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_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file" | 11 python '$__tool_directory__/data_manager_snpEff_databases.py' |
12 </command> | 12 --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar' |
13 <inputs> | 13 '$out_file' |
14 </inputs> | 14 ]]> |
15 <outputs> | 15 </command> |
16 <inputs> | |
17 </inputs> | |
18 <outputs> | |
16 <data name="out_file" format="data_manager_json"/> | 19 <data name="out_file" format="data_manager_json"/> |
17 </outputs> | 20 </outputs> |
18 <tests> | 21 <tests> |
19 <test> | 22 <test> |
20 <output name="out_file"> | 23 <output name="out_file"> |
21 <assert_contents> | 24 <assert_contents> |
22 <!-- Check that a genome was added --> | 25 <!-- Check that a genome was added --> |
23 <has_text text="GRCh38.76" /> | 26 <has_text text="GRCh38.76" /> |
24 </assert_contents> | 27 </assert_contents> |
25 </output> | 28 </output> |
26 </test> | 29 </test> |
27 </tests> | 30 </tests> |
28 <help> | 31 <help> |
29 | 32 |
30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. | 33 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. |
31 It should only need to be run once for a snpEff version, | 34 It should only need to be run once for a snpEff version, |
32 since it populates the SnpEff Download data manager from the snpEff config file. | 35 since it populates the SnpEff Download data manager from the snpEff config file. |
33 | 36 |
34 For information about snpEff: http://snpEff.sourceforge.net | 37 For information about snpEff: http://snpEff.sourceforge.net |
35 | 38 |
36 Please cite: | 39 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] | 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] |
38 | 41 |
39 </help> | 42 </help> |
40 <citations> | 43 <expand macro="citations" /> |
41 <citation type="doi">10.4161/fly.19695</citation> | |
42 </citations> | |
43 </tool> | 44 </tool> |
44 | 45 |