Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
comparison data_manager/data_manager_snpsift_dbnsfp.xml @ 0:0e9e3bb5776a draft
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 10:23:16 -0400 |
parents | |
children | d57ebdd39f0f |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0e9e3bb5776a |
---|---|
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 |