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comparison data_manager/data_manager_snpsift_dbnsfp.xml @ 0:da5d5dc2e55c draft default tip

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author jjohnson
date Wed, 09 Dec 2015 13:58:01 -0500
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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 <command interpreter="python">
7 #import re
8 data_manager_snpsift_dbnsfp.py
9 #if $db.src == 'softgenetics':
10 --softgenetics $db.softgenetics_name
11 #elif $db.src == 'history':
12 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
13 #import os.path
14 --snpsiftdbnsfp $os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)
15 #else
16 --dbnsfp_tabular $db.snpsiftdbnsfp
17 #end if
18 --db_name $db.db_name
19 #if str($db.dbkey).strip() != '':
20 --dbkey "$db.dbkey"
21 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
22 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
23 #end if
24 #end if
25 "$out_file"
26 </command>
27 <inputs>
28 <conditional name="db">
29 <param name="src" type="select" label="Source for dbNSFP file">
30 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
31 <option value="history">from your history</option>
32 </param>
33 <when value="softgenetics">
34 <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site">
35 <help>Download From: ftp://dbnsfp.softgenetics.com/
36 Enter the name of the database, e.g.: dbNSFPv3.0c.zip
37 </help>
38 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
39 </param>
40 </when>
41 <when value="history">
42 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
43 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
44 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
45 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
46 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
47 </param>
48 <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" />
49 </when>
50 </conditional>
51 </inputs>
52
53 <outputs>
54 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
55 </outputs>
56 <stdio>
57 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
58 <exit_code range="1:" level="fatal" description="Error" />
59 </stdio>
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 cite:
78 "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]
79
80 </help>
81 </tool>
82