--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureLinkerLabeled.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,86 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureLinkerLabeled
+
+#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 $rep_param_algorithm_mz_pair_dists:
+    #if " " in str(token):
+      "$token.param_algorithm_mz_pair_dists"
+    #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':
+    #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_algorithm_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate" falsevalue="" 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" 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"/>
+    <param name="param_algorithm_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_algorithm_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_algorithm_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) "/>
+    <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
+      <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_mrm" type="boolean" truevalue="-algorithm:mrm" falsevalue="" 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" format="consensusxml"/>
+  </outputs>
+  <help>**What it does**
+
+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</help>
+  <expand macro="references"/>
+</tool>