Mercurial > repos > eduardo > annotateviz
changeset 3:3302f18f9e16 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
| author | eduardo |
|---|---|
| date | Sat, 17 Jun 2017 15:10:53 -0400 |
| parents | 31e855c95936 |
| children | 92921dfea0b5 |
| files | annotateviz.py annotateviz.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/annotateviz.py Sat Jun 17 14:43:40 2017 -0400 +++ b/annotateviz.py Sat Jun 17 15:10:53 2017 -0400 @@ -19,6 +19,7 @@ parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__) parser.add_argument('-d','--database', help="gffutils sqlite database") parser.add_argument('-j','--json', help="report in json format") + args = parser.parse_args(argv) gffutils.constants.always_return_list = False db = gffutils.interface.FeatureDB(args.database) prediction_list = [] @@ -28,3 +29,5 @@ add_matches(db.features_of_type("PFAM"), prediction_list) fout=open(args.json, 'w') json.dump(prediction_list,fout) +if __name__ == "__main__": + main(sys.argv[1:],sys.stdout)
--- a/annotateviz.xml Sat Jun 17 14:43:40 2017 -0400 +++ b/annotateviz.xml Sat Jun 17 15:10:53 2017 -0400 @@ -14,11 +14,10 @@ --outdir $output.files_path $trackxml && ## $output.files_path/index.html $output; -python $__tool_directory__/annotateviz.py $db > $__tool_directory__/trans.json && +python $__tool_directory__/annotateviz.py -d $db -j ${output.files_path}/trans.json && sed "s@input_db@${__app__.security.encode_id($db.id)}@" $__tool_directory__/static/trinotateviz.html > $output && cp $__tool_directory__/static/js/gff_app.js ${output.files_path} && -cp $__tool_directory__/static/css/main.css ${output.files_path} && -cp $__tool_directory__/trans.json ${output.files_path}; +cp $__tool_directory__/static/css/main.css ${output.files_path}; ]]></command> <configfiles> <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>