# HG changeset patch
# User galaxyp
# Date 1518442933 18000
# Node ID 0604d9974aec55a821a983b2baa2349125a8f580
# Parent  52a38269171f725fea4dd7b171e5f6eaa5cf48a1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74

diff -r 52a38269171f -r 0604d9974aec XTandemAdapter.xml
--- a/XTandemAdapter.xml	Mon Nov 06 07:07:52 2017 -0500
+++ b/XTandemAdapter.xml	Mon Feb 12 08:42:13 2018 -0500
@@ -92,7 +92,7 @@
     $param_enzyme
   #end if
 #end if
-#if $param_missed_cleavages:
+#if str($param_missed_cleavages) != '':
   -missed_cleavages $param_missed_cleavages
 #end if
 #if $param_semi_cleavage:
diff -r 52a38269171f -r 0604d9974aec readme.md
--- a/readme.md	Mon Nov 06 07:07:52 2017 -0500
+++ b/readme.md	Mon Feb 12 08:42:13 2018 -0500
@@ -117,7 +117,14 @@
     [...]
     ]]>
     ```
-    
+ 
+ * In Xtandem Converter and probably in others:
+ 
+    ```
+    #if str($param_missed_cleavages) != '':
+    ```
+    This is because integers needs to be compared as string otherwise `0` becomes `false`.
+ 
  * In `MetaProSIP.xml` add `R` as a requirement:
  
    ```
@@ -164,7 +171,8 @@
     ```
     
 
- * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
+   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
     * SeedListGenerator
     * SpecLibSearcher
     * MapAlignerIdentification