--- a/MRMPairFinder.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MRMPairFinder.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,45 +1,61 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MRMPairFinder" name="MRMPairFinder" version="1.12.0">
-  <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MRMPairFinder</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MRMPairFinder
+<?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: [Utilities]-->
+  <tool id="MRMPairFinder" name="MRMPairFinder" version="2.0.0">
+    <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MRMPairFinder</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MRMPairFinder
 
--in ${param_in}
--pair_in ${param_pair_in}
--out ${param_out}
--feature_out ${param_feature_out}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_pair_in:
+  -pair_in $param_pair_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_feature_out:
+  -feature_out $param_feature_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
 #if $adv_opts.adv_opts_selector=='advanced':
-    -mass_tolerance ${adv_opts.param_mass_tolerance}
-    -RT_tolerance ${adv_opts.param_RT_tolerance}
-    -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance}
+    #if $adv_opts.param_mass_tolerance:
+  -mass_tolerance $adv_opts.param_mass_tolerance
+#end if
+    #if $adv_opts.param_RT_tolerance:
+  -RT_tolerance $adv_opts.param_RT_tolerance
+#end if
+    #if $adv_opts.param_RT_pair_tolerance:
+  -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra." help="(-in)"/>
-    <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in)"/>
-    <expand macro="advanced_options">
-      <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-mass_tolerance)"/>
-      <param name="param_RT_tolerance" type="float" min="0.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file." help="(-RT_tolerance)"/>
-      <param name="param_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have." help="(-RT_pair_tolerance)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output consensusXML file were the pairs of the features will be written to." format="consensusXML"/>
-    <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
-  </outputs>
-  <help>**What it does**
-
-Util which can be used to evaluate labeled pair ratios on MRM features.
+    <inputs>
+      <param format="xml" help="(-in) " label="Input featureXML file containing the features of the MRM experiment spectra" name="param_in" optional="False" type="data"/>
+      <param format="tabular" help="(-pair_in) " label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" name="param_pair_in" optional="False" type="data"/>
+      <expand macro="advanced_options">
+        <param help="(-mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_mass_tolerance" optional="True" type="float" value="0.01"/>
+        <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="0.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
+        <param help="(-RT_pair_tolerance) " label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" min="0.0" name="param_RT_pair_tolerance" optional="True" type="float" value="5.0"/>
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+      <data format="xml" name="param_feature_out"/>
+    </outputs>
+    <help>Util which can be used to evaluate labeled pair ratios on MRM features.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html</help>
+  </tool>