Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_databases.xml @ 5:3d9dd4b9fb09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author | iuc |
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date | Tue, 18 Apr 2017 09:40:03 -0400 |
parents | 847b0f43c0e5 |
children | a6400027d849 |
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4:847b0f43c0e5 | 5:3d9dd4b9fb09 |
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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="4.3k" 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="4.1">snpEff</requirement> | 4 <requirement type="package" version="4.3k">snpeff</requirement> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <command detect_errors="exit_code"><![CDATA[ |
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | 7 python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file' |
8 <exit_code range="1:" level="fatal" description="Error" /> | 8 ]]></command> |
9 </stdio> | 9 <inputs> |
10 <command interpreter="python"> | 10 </inputs> |
11 data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file" | 11 <outputs> |
12 </command> | 12 <data name="out_file" format="data_manager_json"/> |
13 <inputs> | 13 </outputs> |
14 </inputs> | 14 <tests> |
15 <outputs> | 15 <test> |
16 <data name="out_file" format="data_manager_json"/> | 16 <output name="out_file"> |
17 </outputs> | 17 <assert_contents> |
18 <tests> | 18 <!-- Check that a genome was added --> |
19 <test> | 19 <has_text text="GRCh38.76" /> |
20 <output name="out_file"> | 20 </assert_contents> |
21 <assert_contents> | 21 </output> |
22 <!-- Check that a genome was added --> | 22 </test> |
23 <has_text text="GRCh38.76" /> | 23 </tests> |
24 </assert_contents> | 24 <help><![CDATA[ |
25 </output> | 25 This tool updates the list of SnpEff databases for the SnpEff Download data manager. |
26 </test> | 26 It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file. |
27 </tests> | |
28 <help> | |
29 | 27 |
30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager. | 28 For information about SnpEff: http://snpeff.sourceforge.net |
31 It should only need to be run once for a snpEff version, | 29 ]]></help> |
32 since it populates the SnpEff Download data manager from the snpEff config file. | 30 <citations> |
33 | |
34 For information about snpEff: http://snpEff.sourceforge.net | |
35 | |
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] | |
38 | |
39 </help> | |
40 <citations> | |
41 <citation type="doi">10.4161/fly.19695</citation> | 31 <citation type="doi">10.4161/fly.19695</citation> |
42 </citations> | 32 </citations> |
43 </tool> | 33 </tool> |
44 |