# HG changeset patch
# User galaxyp
# Date 1515711133 18000
# Node ID c8b225c69a7fbb32e5a05a5b0d2bcf2e4087413f
# Parent  7b5457bd6112ef62759dd92c4768c2cb6cc88d74
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

diff -r 7b5457bd6112 -r c8b225c69a7f XTandemAdapter.xml
--- a/XTandemAdapter.xml	Thu Nov 09 06:12:04 2017 -0500
+++ b/XTandemAdapter.xml	Thu Jan 11 17:52:13 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 $param_semi_cleavage:
diff -r 7b5457bd6112 -r c8b225c69a7f readme.md
--- a/readme.md	Thu Nov 09 06:12:04 2017 -0500
+++ b/readme.md	Thu Jan 11 17:52:13 2018 -0500
@@ -117,7 +117,14 @@
     [...]
     ]]>
     ```
-    
+ 
+ * In Xtandem Converter and probably in others:
+ 
+    ```
+    #if str($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