Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

comparison data_manager/data_manager_snpsift_dbnsfp.xml @ 4:5ebc15b0bf00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:54:14 -0400
parents 1bf5c56b21a0
children 0a68ef0303c5
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3:1bf5c56b21a0 4:5ebc15b0bf00
2 <description>Install a dbNSFP variant annotation database</description> 2 <description>Install a dbNSFP variant annotation database</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.8.3">pysam</requirement> 4 <requirement type="package" version="0.8.3">pysam</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
8 <exit_code range="1:" level="fatal" description="Error" /> 8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio> 9 </stdio>
10 <command><![CDATA[ 10 <command interpreter="python">
11 python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' 11 #import re
12 data_manager_snpsift_dbnsfp.py
12 #if $db.src == 'softgenetics': 13 #if $db.src == 'softgenetics':
13 --softgenetics '$db.softgenetics_name' 14 --softgenetics "$db.softgenetics_name"
14 #elif $db.src == 'history': 15 #elif $db.src == 'history':
15 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp': 16 #if $db.snpsiftdbnsfp.is_of_type('snpsiftdbnsfp'):
16 #import os.path 17 #import os.path
17 --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)' 18 --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
18 #else 19 #else
19 --dbnsfp_tabular '$db.snpsiftdbnsfp' 20 --dbnsfp_tabular "$db.snpsiftdbnsfp"
20 #end if 21 #end if
21 --db_name '$db.db_name' 22 --db_name "$db.db_name"
22 #if str($db.dbkey).strip() != '': 23 #if str($db.dbkey).strip() != '':
23 --dbkey '$db.dbkey' 24 --dbkey "$db.dbkey"
24 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?': 25 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
25 --dbkey '$db.snpsiftdbnsfp.metadata.dbkey' 26 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
26 #end if 27 #end if
27 #end if 28 #end if
28 '$out_file' 29 "$out_file"
29 ]]> 30 </command>
30 </command>
31 <inputs> 31 <inputs>
32 <conditional name="db"> 32 <conditional name="db">
33 <param name="src" type="select" label="Source for dbNSFP file"> 33 <param name="src" type="select" label="Source for dbNSFP file">
34 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option> 34 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
35 <option value="history">from your history</option> 35 <option value="history">from your history</option>
41 </help> 41 </help>
42 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator> 42 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
43 </param> 43 </param>
44 </when> 44 </when>
45 <when value="history"> 45 <when value="history">
46 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" 46 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
47 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/> 47 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
48 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database"> 48 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
49 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/> 49 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
50 <validator type="regex" message="No whitespace allowed">^\S*$</validator> 50 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
51 </param> 51 </param>
70 70
71 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_ 71 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_
72 It populates data table: snpsift_dbnsfps 72 It populates data table: snpsift_dbnsfps
73 73
74 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP 74 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
75 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP 75 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP
76 76
77 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions. 77 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
78 78
79 </help> 79 </help>
80 <citations> 80 <citations>