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comparison data_manager/data_manager_snpsift_dbnsfp.xml @ 0:5f429f5faba5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
author iuc
date Tue, 07 Jun 2016 10:22:35 -0400
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children 3cf653fe6c46
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-1:000000000000 0:5f429f5faba5
1 <tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.0" tool_type="manage_data">
2 <description>Install a dbNSFP variant annotation database</description>
3 <requirements>
4 <requirement type="package" version="0.7.7">pysam</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio>
10 <command interpreter="python">
11 #import re
12 data_manager_snpsift_dbnsfp.py
13 #if $db.src == 'softgenetics':
14 --softgenetics "$db.softgenetics_name"
15 #elif $db.src == 'history':
16 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
17 #import os.path
18 --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
19 #else
20 --dbnsfp_tabular "$db.snpsiftdbnsfp"
21 #end if
22 --db_name "$db.db_name"
23 #if str($db.dbkey).strip() != '':
24 --dbkey "$db.dbkey"
25 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
26 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
27 #end if
28 #end if
29 "$out_file"
30 </command>
31 <inputs>
32 <conditional name="db">
33 <param name="src" type="select" label="Source for dbNSFP file">
34 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
35 <option value="history">from your history</option>
36 </param>
37 <when value="softgenetics">
38 <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site">
39 <help>Download From: ftp://dbnsfp.softgenetics.com/
40 Enter the name of the database, e.g.: dbNSFPv3.0c.zip
41 </help>
42 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
43 </param>
44 </when>
45 <when value="history">
46 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
47 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
48 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
49 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
50 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
51 </param>
52 <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" />
53 </when>
54 </conditional>
55 </inputs>
56
57 <outputs>
58 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
59 </outputs>
60 <tests>
61 <test>
62 <param name="src" value="history"/>
63 <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/>
64 <param name="dbkey" value="hg19"/>
65 <param name="db_name" value="test_nsfp_tsv" />
66 <output name="out_file" file="test_nsfp.data_manager_json"/>
67 </test>
68 </tests>
69 <help>
70
71 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_
72 It populates data table: snpsift_dbnsfps
73
74 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
75 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP
76
77 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
78
79 </help>
80 <citations>
81 <citation type="doi">DOI: 10.1002/humu.21517</citation>
82 <citation type="doi">DOI: 10.1002/humu.22376</citation>
83 <citation type="doi">DOI: 10.1002/humu.22932</citation>
84 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
85 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
86 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
87 </citations>
88 </tool>
89