# HG changeset patch
# User galaxyp
# Date 1518442959 18000
# Node ID 10cf202b7035d82d2a9def13a7c3a2d97320d139
# Parent  7d0623030f44921f3fdc6b114dc1059969f9b09a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74

diff -r 7d0623030f44 -r 10cf202b7035 FeatureFinderMultiplex.xml
--- a/FeatureFinderMultiplex.xml	Sat Oct 28 04:18:28 2017 -0400
+++ b/FeatureFinderMultiplex.xml	Mon Feb 12 08:42:39 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Quantitation]-->
-<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0">
+<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0.1">
   <description>Determination of peak ratios in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
@@ -24,9 +24,9 @@
 #if $param_out_mzq:
   -out_mzq $param_out_mzq
 #end if
-#if $param_algorithm_labels:
-  -algorithm:labels     "$param_algorithm_labels"
-#end if
+
+-algorithm:labels '$param_algorithm_labels'
+
 #if $param_algorithm_charge:
   -algorithm:charge     "$param_algorithm_charge"
 #end if
diff -r 7d0623030f44 -r 10cf202b7035 readme.md
--- a/readme.md	Sat Oct 28 04:18:28 2017 -0400
+++ b/readme.md	Mon Feb 12 08:42:39 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