Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_databases.xml @ 4:847b0f43c0e5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:14:37 -0400 |
parents | e5a471c4630e |
children | 3d9dd4b9fb09 |
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3:e5a471c4630e | 4:847b0f43c0e5 |
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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 |