# HG changeset patch
# User galaxyp
# Date 1515711116 18000
# Node ID d92d43ce63ce063aed89c06c4b963bf97a39345d
# Parent  ee74aa49131be26f341be31e9f34625992eacd89
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

diff -r ee74aa49131b -r d92d43ce63ce IDMapper.xml
--- a/IDMapper.xml	Sat Oct 28 05:13:22 2017 -0400
+++ b/IDMapper.xml	Thu Jan 11 17:51:56 2018 -0500
@@ -91,7 +91,7 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" metadata_source="param_in" format="input"/>
+    <data name="param_out" metadata_source="param_in" format_source="param_in"/>
   </outputs>
   <help>Assigns protein/peptide identifications to features or consensus features.
 
diff -r ee74aa49131b -r d92d43ce63ce readme.md
--- a/readme.md	Sat Oct 28 05:13:22 2017 -0400
+++ b/readme.md	Thu Jan 11 17:51:56 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