# HG changeset patch
# User bgruening
# Date 1381739812 14400
# Node ID d26e8aa37ce994de6a662bc4a48adab35210efa3
# Parent  225d40beff1a66776fc03e8a90013ec048eb73ee
Uploaded

diff -r 225d40beff1a -r d26e8aa37ce9 antismash.xml
--- a/antismash.xml	Mon Oct 14 03:26:11 2013 -0400
+++ b/antismash.xml	Mon Oct 14 04:36:52 2013 -0400
@@ -14,7 +14,10 @@
     <command>
         #import os, glob
         #set $outputfolder = $html.files_path
-        #if $infile.ext == 'genbank':
+        #if str($infile.ext) == 'genbank':
+            #set $file_extension = 'gb'
+        #else:
+            ## TODO add embl as input file
             #set $file_extension = 'gb'
         #end if
 
diff -r 225d40beff1a -r d26e8aa37ce9 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Oct 14 04:36:52 2013 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="AntiSmash requires the Galaxy applicable data formats used by Emboss tools, especially genbank.">
+    <repository changeset_revision="9f36ad2af086" name="emboss_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 225d40beff1a -r d26e8aa37ce9 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 14 03:26:11 2013 -0400
+++ b/tool_dependencies.xml	Mon Oct 14 04:36:52 2013 -0400
@@ -130,6 +130,15 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
+                        we need to copy this plugin into the correct location.
+                    -->
+                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
+                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
+                    <action type="move_file">
+                        <source>__init__.py</source>
+                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
+                    </action>
                     <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
@@ -137,13 +146,6 @@
                     <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
-                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
-                        we need to copy this plugin into the correct location.
-                    -->
-                    <action type="move_directory_files">
-                        <source_directory>$REPOSITORY_INSTALL_DIR/src/</source_directory>
-                        <destination_directory>$INSTALL_DIR/antismash/output_modules/</destination_directory>
-                    </action>
                 </actions>
                 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
                 <actions architecture="i386" os="linux">