# HG changeset patch
# User sanbi-uwc
# Date 1463391910 14400
# Node ID 9cc174f0fb9f433163efc912a9d2f62a5a650fb7
# Parent  56555326a05697c4011d60b8c7e5ab8e6bee45c9
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 2b6755be1c76f3e4209f9723e7f50f945939244f

diff -r 56555326a056 -r 9cc174f0fb9f build_ctb_gene.py
--- a/build_ctb_gene.py	Mon May 16 05:32:38 2016 -0400
+++ b/build_ctb_gene.py	Mon May 16 05:45:10 2016 -0400
@@ -12,7 +12,8 @@
 
 def build_ctb_gene(output_file1, output_dir, input_file, mount_point):
     # cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
-    cmdline_str = "echo goterms"
+    cmdline_str = "echo %s" % input_file
+    output_dir = mount_point
     build_ctb = False
     try:
         os.system(cmdline_str)
diff -r 56555326a056 -r 9cc174f0fb9f build_ctb_gene.xml
--- a/build_ctb_gene.xml	Mon May 16 05:32:38 2016 -0400
+++ b/build_ctb_gene.xml	Mon May 16 05:45:10 2016 -0400
@@ -9,8 +9,7 @@
         <exit_code range="1:" />
     </stdio>
     <command interpreter="python">
-        build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --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 ${db_settings.neo4j_db_port}
+        build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --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" />