Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
changeset 4:47f276ffcbfc draft
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 18:15:17 -0400 |
| parents | 0e9624bcd707 |
| children | 09f9bfb2b33b |
| files | data_manager/data_manager_snpsift_dbnsfp.py data_manager/data_manager_snpsift_dbnsfp.xml tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 20 insertions(+), 19 deletions(-) [+] |
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--- a/data_manager/data_manager_snpsift_dbnsfp.py Mon Oct 31 08:13:28 2016 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.py Tue Apr 04 18:15:17 2017 -0400 @@ -197,5 +197,6 @@ # save info to json file open(filename, 'wb').write(json.dumps(data_manager_dict)) + if __name__ == "__main__": main()
--- a/data_manager/data_manager_snpsift_dbnsfp.xml Mon Oct 31 08:13:28 2016 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.xml Tue Apr 04 18:15:17 2017 -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><![CDATA[ - python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' + <command interpreter="python"> + #import re + 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': + #if $db.snpsiftdbnsfp.is_of_type('snpsiftdbnsfp'): #import os.path - --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)' - #else - --dbnsfp_tabular '$db.snpsiftdbnsfp' + --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)" + #else + --dbnsfp_tabular "$db.snpsiftdbnsfp" #end if - --db_name '$db.db_name' - #if str($db.dbkey).strip() != '': - --dbkey '$db.dbkey' + --db_name "$db.db_name" + #if str($db.dbkey).strip() != '': + --dbkey "$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"> @@ -43,7 +43,7 @@ </param> </when> <when value="history"> - <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" + <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/> <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database"> <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/> @@ -72,7 +72,7 @@ It populates data table: snpsift_dbnsfps .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP -.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP +.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
--- a/tool_data_table_conf.xml.sample Mon Oct 31 08:13:28 2016 -0400 +++ b/tool_data_table_conf.xml.sample Tue Apr 04 18:15:17 2017 -0400 @@ -1,5 +1,5 @@ <tables> - <table name="snpsift_dbnsfps" comment_char="#"> + <table name="snpsift_dbnsfps" comment_char="#" allow_duplicate_entries="False"> <columns>key, build, name, value, annotations</columns> <file path="tool-data/snpsift_dbnsfps.loc" /> </table>