# HG changeset patch
# User sanbi-uwc
# Date 1463474381 14400
# Node ID 7d49ea27d9f64004ec745d92ed8da6964fb0b441
# Parent  51769181245290f18f7ca6dbd5b06912b8bb140e
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 9ba2424793e47546990c750ac5f1129bd1e3a77c

diff -r 517691812452 -r 7d49ea27d9f6 build_ctb_gene.py
--- 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()
 
diff -r 517691812452 -r 7d49ea27d9f6 build_ctb_gene.xml
--- 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>