Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 13:3ef417806df9 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 3dd4b95732efe95365fc09bfcdfb917c25b2796e
| author | sanbi-uwc |
|---|---|
| date | Tue, 17 May 2016 07:34:13 -0400 |
| parents | 7d49ea27d9f6 |
| children | 4caf3e2d10e8 |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/build_ctb_gene.py Tue May 17 04:39:41 2016 -0400 +++ b/build_ctb_gene.py Tue May 17 07:34:13 2016 -0400 @@ -27,15 +27,18 @@ def build_ctb_gene(self): #cmdline_str = "build_ctb_gene goterms ${}".format(input_file) #cmdline_str = "build_ctb_gene goterms --help" - cmdline_str = "touch /tmp/foo.bar >> %s" %self.args.outputdir + cmdline_str = "touch /tmp/foo.bar" + build_ctb = False cmdline_str = self.newSplit(cmdline_str) try: check_call(cmdline_str) + #build_ctb = True except CalledProcessError: print("Error running the build_ctb_gene gotermS", file=sys.stderr) self.copy_output_file_to_dataset() - self.args.output_file1 = self.args.outputdir + #self.args.outputdir = "<html><body>The Output of the Neo4J DB</body></html>" + #return self.args.outputdir def newSplit(self, value): lex = shlex.shlex(value) @@ -48,7 +51,6 @@ ''' Retrieves the output files from the output directory and copies them to the Galaxy output files ''' - # retrieve neo4j files to the working gx directory result_file = glob.glob(self.args.mount_point + '/*') for file_name in result_file: @@ -61,7 +63,7 @@ def main(): parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags") - parser.add_argument('output_file1') + #parser.add_argument('--outputfile') parser.add_argument('--outputdir') parser.add_argument('--input_file') parser.add_argument('--mount_point') @@ -84,5 +86,5 @@ ctb_gene_runner = BuildCtbRunner(args) ctb_gene_runner.build_ctb_gene() -if __name__ == "__main__": main() +if __name__ == "__main__": main() \ No newline at end of file
--- a/build_ctb_gene.xml Tue May 17 04:39:41 2016 -0400 +++ b/build_ctb_gene.xml Tue May 17 07:34:13 2016 -0400 @@ -9,8 +9,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} - + build_ctb_gene.py --outputdir "${os.path.join($outputFile1.files_path,'neo4jdb')}" --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" /> @@ -23,8 +22,7 @@ </section> </inputs> <outputs> - <data format="neo4j" name="outputFile1"/> - <data format="neostore" name="outputFile2"/> + <data format="neostore" name="outputFile1"/> </outputs> <help>Help!</help> <citations>