--- a/cloudmap.xml	Fri Sep 11 16:25:49 2015 +0200
+++ b/cloudmap.xml	Tue Sep 22 22:36:41 2015 +0200
@@ -1,12 +1,9 @@
 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.0">
   <description>Map causative mutations by multi-variant linkage analysis.</description>
-  <macros>
-    <import>toolshed_macros.xml</import>
-  </macros>
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
-    mimodd map "${opt.source.ifile}" ${opt.mode}
+    mimodd map ${opt.mode} "${opt.source.ifile}"
     #if $str($opt.source.sample):
       -m "${opt.source.sample}"
     #end if
@@ -60,6 +57,7 @@
   </command>
 
   <macros>
+    <import>toolshed_macros.xml</import>
     <macro name="svd_unconditional">
       <expand macro="hidden_vaf_algo_params" />
       <expand macro="seqdict_param" />
@@ -122,7 +120,7 @@
       <param name="infer_missing" type="hidden" value="" />
     </macro>
     <macro name="bins">
-      <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed.">
+      <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed.">
         <param name="bin_size" type="text" />
       </repeat>
     </macro>

--- a/tool_dependencies.xml	Fri Sep 11 16:25:49 2015 +0200
+++ b/tool_dependencies.xml	Tue Sep 22 22:36:41 2015 +0200
@@ -29,8 +29,9 @@
         <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
       <!-- make MiModD's wrapped binaries executable -->
         <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action>
-        
-        
+      <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
+        <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
+                
         <action type="set_environment">
       <!-- make the mimodd entry script discoverable -->
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>