--- a/FeatureLinkerUnlabeled.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FeatureLinkerUnlabeled.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,64 +1,109 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0">
-  <description>Groups corresponding features from multiple maps.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FeatureLinkerUnlabeled
+<?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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.0.0">
+    <description>Groups corresponding features from multiple maps.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FeatureLinkerUnlabeled
 
--in ${param_in}
--out ${param_out}
-${param_keep_subelements}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:second_nearest_gap ${param_second_nearest_gap}
-${param_use_identifications}
-${param_ignore_charge}
--algorithm:distance_RT:max_difference ${param_max_difference}
--algorithm:distance_MZ:max_difference ${param_max_difference}
--algorithm:distance_MZ:unit ${param_unit}
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_keep_subelements:
+  -keep_subelements
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_second_nearest_gap:
+  -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
+#end if
+#if $param_algorithm_use_identifications:
+  -algorithm:use_identifications
+#end if
+#if $param_algorithm_ignore_charge:
+  -algorithm:ignore_charge
+#end if
+#if $param_algorithm_distance_RT_max_difference:
+  -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
+#end if
+#if $param_algorithm_distance_MZ_max_difference:
+  -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
+#end if
+#if $param_algorithm_distance_MZ_unit:
+  -algorithm:distance_MZ:unit
+  #if &quot; &quot; in str($param_algorithm_distance_MZ_unit):
+    &quot;$param_algorithm_distance_MZ_unit&quot;
+  #else
+    $param_algorithm_distance_MZ_unit
+  #end if
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
-    -algorithm:distance_RT:weight ${adv_opts.param_weight}
-    -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
-    -algorithm:distance_MZ:weight ${adv_opts.param_weight}
-    -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
-    -algorithm:distance_intensity:weight ${adv_opts.param_weight}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_distance_RT_exponent:
+  -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
+#end if
+    #if $adv_opts.param_algorithm_distance_RT_weight:
+  -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
+#end if
+    #if $adv_opts.param_algorithm_distance_MZ_exponent:
+  -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
+#end if
+    #if $adv_opts.param_algorithm_distance_MZ_weight:
+  -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
+#end if
+    #if $adv_opts.param_algorithm_distance_intensity_exponent:
+  -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
+#end if
+    #if $adv_opts.param_algorithm_distance_intensity_weight:
+  -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
-    <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." help="(-keep_subelements)"/>
-    <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
-    <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
-    <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
-    <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
-    <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
-    <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
-      <option value="Da">Da</option>
-      <option value="ppm">ppm</option>
-    </param>
-    <expand macro="advanced_options">
-      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
-      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
-      <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
-      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
-      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
-      <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file" format="consensusXML"/>
-  </outputs>
-  <help>**What it does**
-
-Groups corresponding features from multiple maps.
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/>
+      <param help="(-second_nearest_gap) " label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" min="1.0" name="param_algorithm_second_nearest_gap" optional="True" type="float" value="2.0"/>
+      <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" name="param_algorithm_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/>
+      <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
+      <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
+      <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da">
+        <option value="Da">Da</option>
+        <option value="ppm">ppm</option>
+      </param>
+      <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 help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_RT_exponent" optional="True" type="float" value="1.0"/>
+        <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/>
+        <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
+        <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/>
+        <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
+        <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+    </outputs>
+    <help>Groups corresponding features from multiple maps.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html</help>
+  </tool>