--- a/FeatureLinkerUnlabeledKD.xml	Thu Jan 11 18:02:12 2018 -0500
+++ b/FeatureLinkerUnlabeledKD.xml	Mon Feb 12 13:02:25 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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
-<tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.2.0">
+<tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.3.0">
   <description>Groups corresponding features from multiple maps.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token>
@@ -19,15 +19,12 @@
 #if $param_out:
   -out $param_out
 #end if
+#if $param_design:
+  -design $param_design
+#end if
 #if $param_keep_subelements:
   -keep_subelements
 #end if
-#if $param_algorithm_rt_tol:
-  -algorithm:rt_tol $param_algorithm_rt_tol
-#end if
-#if $param_algorithm_mz_tol:
-  -algorithm:mz_tol $param_algorithm_mz_tol
-#end if
 #if $param_algorithm_mz_unit:
   -algorithm:mz_unit
   #if " " in str($param_algorithm_mz_unit):
@@ -36,29 +33,41 @@
     $param_algorithm_mz_unit
   #end if
 #end if
-#if $param_algorithm_warp:
-  -algorithm:warp
-  #if " " in str($param_algorithm_warp):
-    "$param_algorithm_warp"
+#if $param_algorithm_nr_partitions:
+  -algorithm:nr_partitions $param_algorithm_nr_partitions
+#end if
+#if $param_algorithm_warp_enabled:
+  -algorithm:warp:enabled
+  #if " " in str($param_algorithm_warp_enabled):
+    "$param_algorithm_warp_enabled"
   #else
-    $param_algorithm_warp
+    $param_algorithm_warp_enabled
   #end if
 #end if
-#if $param_algorithm_nr_partitions:
-  -algorithm:nr_partitions $param_algorithm_nr_partitions
+#if $param_algorithm_warp_rt_tol:
+  -algorithm:warp:rt_tol $param_algorithm_warp_rt_tol
+#end if
+#if $param_algorithm_warp_mz_tol:
+  -algorithm:warp:mz_tol $param_algorithm_warp_mz_tol
+#end if
+#if $param_algorithm_link_rt_tol:
+  -algorithm:link:rt_tol $param_algorithm_link_rt_tol
+#end if
+#if $param_algorithm_link_mz_tol:
+  -algorithm:link:mz_tol $param_algorithm_link_mz_tol
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
   -force
 #end if
-    #if $adv_opts.param_algorithm_max_pairwise_log_fc:
-  -algorithm:max_pairwise_log_fc $adv_opts.param_algorithm_max_pairwise_log_fc
+    #if $adv_opts.param_algorithm_warp_max_pairwise_log_fc:
+  -algorithm:warp:max_pairwise_log_fc $adv_opts.param_algorithm_warp_max_pairwise_log_fc
 #end if
-    #if $adv_opts.param_algorithm_min_rel_cc_size:
-  -algorithm:min_rel_cc_size $adv_opts.param_algorithm_min_rel_cc_size
+    #if $adv_opts.param_algorithm_warp_min_rel_cc_size:
+  -algorithm:warp:min_rel_cc_size $adv_opts.param_algorithm_warp_min_rel_cc_size
 #end if
-    #if $adv_opts.param_algorithm_max_nr_conflicts:
-  -algorithm:max_nr_conflicts $adv_opts.param_algorithm_max_nr_conflicts
+    #if $adv_opts.param_algorithm_warp_max_nr_conflicts:
+  -algorithm:warp:max_nr_conflicts $adv_opts.param_algorithm_warp_max_nr_conflicts
 #end if
     #if $adv_opts.param_algorithm_distance_RT_exponent:
   -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
@@ -122,23 +131,26 @@
         </valid>
       </sanitizer>
     </param>
+    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
     <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" 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_algorithm_rt_tol" type="float" min="0.0" optional="True" value="60.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
-    <param name="param_algorithm_mz_tol" type="float" min="0.0" optional="True" value="15.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
     <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of m/z tolerance" help="(-mz_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
-    <param name="param_algorithm_warp" display="radio" type="select" optional="False" value="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help="(-warp) ">
+    <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="Number of partitions in m/z space" help="(-nr_partitions) "/>
+    <param name="param_algorithm_warp_enabled" display="radio" type="select" optional="False" value="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help="(-enabled) ">
       <option value="true" selected="true">true</option>
       <option value="false">false</option>
     </param>
-    <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="Number of partitions in m/z space" help="(-nr_partitions) "/>
+    <param name="param_algorithm_warp_rt_tol" type="float" min="0.0" optional="True" value="100.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
+    <param name="param_algorithm_warp_mz_tol" type="float" min="0.0" optional="True" value="5.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
+    <param name="param_algorithm_link_rt_tol" type="float" min="0.0" optional="True" value="30.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
+    <param name="param_algorithm_link_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
     <expand macro="advanced_options">
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-      <param name="param_algorithm_max_pairwise_log_fc" type="float" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="(-max_pairwise_log_fc) Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value &lt; 0 disables the FC check"/>
-      <param name="param_algorithm_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help="(-min_rel_cc_size) "/>
-      <param name="param_algorithm_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="Only relevant during RT alignment ('warp' set to 'true'): Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help="(-max_nr_conflicts) "/>
+      <param name="param_algorithm_warp_max_pairwise_log_fc" type="float" value="0.5" label="Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="(-max_pairwise_log_fc) Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value &lt; 0 disables the FC check"/>
+      <param name="param_algorithm_warp_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help="(-min_rel_cc_size) "/>
+      <param name="param_algorithm_warp_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help="(-max_nr_conflicts) "/>
       <param name="param_algorithm_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" 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)" help="(-exponent) "/>
       <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
       <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" 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)" help="(-exponent) "/>