| Previous changeset 2:3d4cd0e3891f (2016-06-10) Next changeset 4:47f276ffcbfc (2017-04-04) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit de422632b9310905f8e9d44faee9ff768752968f |
|
modified:
data_manager/data_manager_snpsift_dbnsfp.xml |
|
removed:
data_manager/.data_manager_snpsift_dbnsfp.py.swp |
| b |
| diff -r 3d4cd0e3891f -r 0e9624bcd707 data_manager/.data_manager_snpsift_dbnsfp.py.swp |
| b |
| Binary file data_manager/.data_manager_snpsift_dbnsfp.py.swp has changed |
| b |
| diff -r 3d4cd0e3891f -r 0e9624bcd707 data_manager/data_manager_snpsift_dbnsfp.xml --- a/data_manager/data_manager_snpsift_dbnsfp.xml Fri Jun 10 08:25:06 2016 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.xml Mon Oct 31 08:13:28 2016 -0400 |
| [ |
| @@ -4,30 +4,30 @@ <requirement type="package" version="0.8.3">pysam</requirement> </requirements> <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python"> - #import re - data_manager_snpsift_dbnsfp.py + <command><![CDATA[ + python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' #if $db.src == 'softgenetics': - --softgenetics "$db.softgenetics_name" + --softgenetics '$db.softgenetics_name' #elif $db.src == 'history': #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp': #import os.path - --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)" + --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)' #else - --dbnsfp_tabular "$db.snpsiftdbnsfp" + --dbnsfp_tabular '$db.snpsiftdbnsfp' #end if - --db_name "$db.db_name" + --db_name '$db.db_name' #if str($db.dbkey).strip() != '': - --dbkey "$db.dbkey" + --dbkey '$db.dbkey' #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?': - --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" + --dbkey '$db.snpsiftdbnsfp.metadata.dbkey' #end if #end if - "$out_file" - </command> + '$out_file' + ]]> + </command> <inputs> <conditional name="db"> <param name="src" type="select" label="Source for dbNSFP file"> |