Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

comparison data_manager/data_manager_snpsift_dbnsfp.xml @ 3:1bf5c56b21a0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:12:30 -0400
parents 3cf653fe6c46
children 5ebc15b0bf00
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equal deleted inserted replaced
2:1adeb79c05f8 3:1bf5c56b21a0
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 interpreter="python"> 10 <command><![CDATA[
11 #import re 11 python '$__tool_directory__/data_manager_snpsift_dbnsfp.py'
12 data_manager_snpsift_dbnsfp.py
13 #if $db.src == 'softgenetics': 12 #if $db.src == 'softgenetics':
14 --softgenetics "$db.softgenetics_name" 13 --softgenetics '$db.softgenetics_name'
15 #elif $db.src == 'history': 14 #elif $db.src == 'history':
16 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp': 15 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
17 #import os.path 16 #import os.path
18 --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)" 17 --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)'
19 #else 18 #else
20 --dbnsfp_tabular "$db.snpsiftdbnsfp" 19 --dbnsfp_tabular '$db.snpsiftdbnsfp'
21 #end if 20 #end if
22 --db_name "$db.db_name" 21 --db_name '$db.db_name'
23 #if str($db.dbkey).strip() != '': 22 #if str($db.dbkey).strip() != '':
24 --dbkey "$db.dbkey" 23 --dbkey '$db.dbkey'
25 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?': 24 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
26 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" 25 --dbkey '$db.snpsiftdbnsfp.metadata.dbkey'
27 #end if 26 #end if
28 #end if 27 #end if
29 "$out_file" 28 '$out_file'
30 </command> 29 ]]>
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>