# HG changeset patch
# User sanbi-uwc
# Date 1463574516 14400
# Node ID e6d850bb9fb6774c35314a524f8233d2328852b8
# Parent  4caf3e2d10e8f5e2f7214452b3c90b2d97c65c90
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit c78b1532031ee875ff51cb2a4c73f4577bd07839

diff -r 4caf3e2d10e8 -r e6d850bb9fb6 build_ctb_gene.py
--- a/build_ctb_gene.py	Wed May 18 04:49:51 2016 -0400
+++ b/build_ctb_gene.py	Wed May 18 08:28:36 2016 -0400
@@ -55,6 +55,7 @@
 
 def main():
     parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
+    parser.add_argument('--outputfile')
     parser.add_argument('--outputdir')
     parser.add_argument('--input_file')
     parser.add_argument('--mount_point')
diff -r 4caf3e2d10e8 -r e6d850bb9fb6 build_ctb_gene.xml
--- a/build_ctb_gene.xml	Wed May 18 04:49:51 2016 -0400
+++ b/build_ctb_gene.xml	Wed May 18 08:28:36 2016 -0400
@@ -9,7 +9,7 @@
         <exit_code range="1:" />
     </stdio>
     <command interpreter="python">
-        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} &gt; ${outputFile1}
+        build_ctb_gene.py --outputfile "${outputFile1}" --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} &gt; ${outputFile1}
     </command>
     <inputs>
         <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />