--- a/FeatureLinkerLabeled.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FeatureLinkerLabeled.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,49 +1,86 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="1.12.0">
-  <description>Groups corresponding isotope-labeled features in a feature map.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FeatureLinkerLabeled
+<?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: [Map Alignment]-->
+  <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.0.0">
+    <description>Groups corresponding isotope-labeled features in a feature map.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FeatureLinkerLabeled
 
--in ${param_in}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
-${param_rt_estimate}
--algorithm:rt_pair_dist ${param_rt_pair_dist}
--algorithm:rt_dev_low ${param_rt_dev_low}
--algorithm:rt_dev_high ${param_rt_dev_high}
--algorithm:mz_pair_dists ${param_mz_pair_dists}
--algorithm:mz_dev ${param_mz_dev}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_rt_estimate:
+  -algorithm:rt_estimate
+#end if
+#if $param_algorithm_rt_pair_dist:
+  -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
+#end if
+#if $param_algorithm_rt_dev_low:
+  -algorithm:rt_dev_low $param_algorithm_rt_dev_low
+#end if
+#if $param_algorithm_rt_dev_high:
+  -algorithm:rt_dev_high $param_algorithm_rt_dev_high
+#end if
+
+#if $rep_param_algorithm_mz_pair_dists:
+-algorithm:mz_pair_dists
+  #for token in $rep_param_algorithm_mz_pair_dists:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_algorithm_mz_pair_dists&quot;
+    #else
+      $token.param_algorithm_mz_pair_dists
+    #end if
+  #end for
+#end if
+#if $param_algorithm_mz_dev:
+  -algorithm:mz_dev $param_algorithm_mz_dev
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    ${adv_opts.param_mrm}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_mrm:
+  -algorithm:mrm
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML" optional="False" label="Input file" help="(-in)"/>
-    <param name="param_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate true" falsevalue="-algorithm:rt_estimate false" checked="true" optional="True" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance." help="(-rt_estimate)"/>
-    <param name="param_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist)"/>
-    <param name="param_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low)"/>
-    <param name="param_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high)"/>
-    <param name="param_mz_pair_dists" type="text" size="20" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)" help="(-mz_pair_dists)"/>
-    <param name="param_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance#br#" help="(-mz_dev)"/>
-    <expand macro="advanced_options">
-      <param name="param_mrm" type="boolean" truevalue="-algorithm:mrm true" falsevalue="-algorithm:mrm false" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file" format="consensusXML"/>
-  </outputs>
-  <help>**What it does**
-
-Groups corresponding isotope-labeled features in a feature map.
+    <inputs>
+      <param format="xml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
+      <param checked="true" falsevalue="" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" name="param_algorithm_rt_estimate" optional="True" truevalue="-algorithm:rt_estimate" type="boolean"/>
+      <param help="(-rt_pair_dist) " label="optimal pair distance in RT [sec] from light to heavy feature" name="param_algorithm_rt_pair_dist" type="float" value="-20.0"/>
+      <param help="(-rt_dev_low) " label="maximum allowed deviation below optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_low" optional="True" type="float" value="15.0"/>
+      <param help="(-rt_dev_high) " label="maximum allowed deviation above optimal retention time distance" min="0.0" name="param_algorithm_rt_dev_high" optional="True" type="float" value="15.0"/>
+      <repeat max="1" min="0" name="rep_param_algorithm_mz_pair_dists" title="param_algorithm_mz_pair_dists">
+        <param help="(-mz_pair_dists) by division through charge)" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." name="param_algorithm_mz_pair_dists" size="30" type="text" value="4.0">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-mz_dev) " label="maximum allowed deviation from optimal m/z distance" min="0.0" name="param_algorithm_mz_dev" optional="True" type="float" value="0.05"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param checked="false" falsevalue="" help="(-mrm) " label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" name="param_algorithm_mrm" optional="True" truevalue="-algorithm:mrm" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+    </outputs>
+    <help>Groups corresponding isotope-labeled features in a feature map.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
+  </tool>