Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 12:7d49ea27d9f6 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 9ba2424793e47546990c750ac5f1129bd1e3a77c
author | sanbi-uwc |
---|---|
date | Tue, 17 May 2016 04:39:41 -0400 |
parents | 517691812452 |
children | 3ef417806df9 |
files | build_ctb_gene.py build_ctb_gene.xml |
diffstat | 2 files changed, 4 insertions(+), 39 deletions(-) [+] |
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--- a/build_ctb_gene.py Tue May 17 03:45:58 2016 -0400 +++ b/build_ctb_gene.py Tue May 17 04:39:41 2016 -0400 @@ -24,15 +24,13 @@ #assert args != None self.args = args - def build_ctb_gene(self, output_file1, output_dir, input_file, mount_point): + def build_ctb_gene(self): #cmdline_str = "build_ctb_gene goterms ${}".format(input_file) #cmdline_str = "build_ctb_gene goterms --help" - cmdline_str = "touch /tmp/foo.bar" - build_ctb = False + cmdline_str = "touch /tmp/foo.bar >> %s" %self.args.outputdir cmdline_str = self.newSplit(cmdline_str) try: check_call(cmdline_str) - #build_ctb = True except CalledProcessError: print("Error running the build_ctb_gene gotermS", file=sys.stderr) @@ -84,8 +82,7 @@ os.makedirs(args.outputdir) ctb_gene_runner = BuildCtbRunner(args) - ctb_gene_runner.build_ctb_gene(args.output_file1, args.outputdir, args.input_file, args.mount_point) - + ctb_gene_runner.build_ctb_gene() if __name__ == "__main__": main()
--- a/build_ctb_gene.xml Tue May 17 03:45:58 2016 -0400 +++ b/build_ctb_gene.xml Tue May 17 04:39:41 2016 -0400 @@ -10,6 +10,7 @@ </stdio> <command interpreter="python"> build_ctb_gene.py '${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} + </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" /> @@ -24,39 +25,6 @@ <outputs> <data format="neo4j" name="outputFile1"/> <data format="neostore" name="outputFile2"/> - <!--<data format="neostore" name="outputFile3"/> - <data format="neostore" name="outputFile4"/> - <data format="neostore" name="outputFile5"/> - <data format="neostore" name="outputFile6"/> - <data format="neostore" name="outputFile7"/> - <data format="neostore" name="outputFile8"/> - <data format="neostore" name="outputFile9"/> - <data format="neostore" name="outputFile10"/> - <data format="neostore" name="outputFile11"/> - <data format="neostore" name="outputFile12"/> - <data format="neostore" name="outputFile13"/> - <data format="neostore" name="outputFile14"/> - <data format="neostore" name="outputFile15"/> - <data format="neostore" name="outputFile16"/> - <data format="neostore" name="outputFile17"/> - <data format="neostore" name="outputFile18"/> - <data format="neostore" name="outputFile19"/> - <data format="neostore" name="outputFile20"/> - <data format="neostore" name="outputFile21"/> - <data format="neostore" name="outputFile22"/> - <data format="neostore" name="outputFile23"/> - <data format="neostore" name="outputFile24"/> - <data format="neostore" name="outputFile25"/> - <data format="neostore" name="outputFile26"/> - <data format="neostore" name="outputFile27"/> - <data format="neostore" name="outputFile28"/> - <data format="neostore" name="outputFile29"/> - <data format="neostore" name="outputFile30"/> - <data format="neostore" name="outputFile31"/> - <data format="neostore" name="outputFile32"/> - <data format="neostore" name="outputFile33"/> - <data format="neostore" name="outputFile34"/> - <data format="neostore" name="outputFile35"/> --> </outputs> <help>Help!</help> <citations>