--- a/MapAlignerIdentification.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MapAlignerIdentification.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,66 +1,153 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="1.12.0">
-  <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MapAlignerIdentification</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MapAlignerIdentification
+<?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="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
+    <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MapAlignerIdentification</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MapAlignerIdentification
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+
+#if $rep_param_out:
+-out
+  #for token in $rep_param_out:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_out&quot;
+    #else
+      $token.param_out
+    #end if
+  #end for
+#end if
 
--in ${param_in}
--out ${param_out}
--trafo_out ${param_trafo_out}
--threads \${GALAXY_SLOTS:-24} 
--reference:file ${param_file}
--reference:index ${param_index}
--algorithm:peptide_score_threshold ${param_peptide_score_threshold}
--algorithm:min_run_occur ${param_min_run_occur}
--algorithm:max_rt_shift ${param_max_rt_shift}
-${param_use_unassigned_peptides}
-${param_use_feature_rt}
--model:type ${param_type}
-${param_symmetric_regression}
--model:interpolated:interpolation_type ${param_interpolation_type}
+#if $rep_param_trafo_out:
+-trafo_out
+  #for token in $rep_param_trafo_out:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_trafo_out&quot;
+    #else
+      $token.param_trafo_out
+    #end if
+  #end for
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_reference_file:
+  -reference:file $param_reference_file
+#end if
+#if $param_reference_index:
+  -reference:index $param_reference_index
+#end if
+#if $param_algorithm_peptide_score_threshold:
+  -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
+#end if
+#if $param_algorithm_min_run_occur:
+  -algorithm:min_run_occur $param_algorithm_min_run_occur
+#end if
+#if $param_algorithm_max_rt_shift:
+  -algorithm:max_rt_shift $param_algorithm_max_rt_shift
+#end if
+#if $param_algorithm_use_unassigned_peptides:
+  -algorithm:use_unassigned_peptides
+#end if
+#if $param_algorithm_use_feature_rt:
+  -algorithm:use_feature_rt
+#end if
+#if $param_model_type:
+  -model:type
+  #if &quot; &quot; in str($param_model_type):
+    &quot;$param_model_type&quot;
+  #else
+    $param_model_type
+  #end if
+#end if
+#if $param_model_linear_symmetric_regression:
+  -model:linear:symmetric_regression
+#end if
+#if $param_model_b_spline_wavelength:
+  -model:b_spline:wavelength $param_model_b_spline_wavelength
+#end if
+#if $param_model_b_spline_num_nodes:
+  -model:b_spline:num_nodes $param_model_b_spline_num_nodes
+#end if
+#if $param_model_b_spline_extrapolate:
+  -model:b_spline:extrapolate
+  #if &quot; &quot; in str($param_model_b_spline_extrapolate):
+    &quot;$param_model_b_spline_extrapolate&quot;
+  #else
+    $param_model_b_spline_extrapolate
+  #end if
+#end if
+#if $param_model_b_spline_boundary_condition:
+  -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
+#end if
+#if $param_model_interpolated_interpolation_type:
+  -model:interpolated:interpolation_type
+  #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
+    &quot;$param_model_interpolated_interpolation_type&quot;
+  #else
+    $param_model_interpolated_interpolation_type
+  #end if
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" size="20" label="Input files separated by blanks (all must have the same file type)" help="(-in)"/>
-    <param name="param_file" type="data" format="featureXML,consensusXML,idXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file)"/>
-    <param name="param_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." help="(-index)"/>
-    <param name="param_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment.#br#Select a value that allows only 'high confidence' matches." help="(-peptide_score_threshold)"/>
-    <param name="param_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.#br#Unless you have very few runs or identifications, increase this value to focus on more informative peptides." help="(-min_run_occur)"/>
-    <param name="param_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.#br#If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale." help="(-max_rt_shift)"/>
-    <param name="param_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides true" falsevalue="-algorithm:use_unassigned_peptides false" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used." help="(-use_unassigned_peptides)"/>
-    <param name="param_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt true" falsevalue="-algorithm:use_feature_rt false" checked="false" optional="True" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.#br#Precludes 'use_unassigned_peptides'." help="(-use_feature_rt)"/>
-    <param name="param_type" type="select" optional="True" value="interpolated" label="Type of model" help="(-type)">
-      <option value="linear">linear</option>
-      <option value="b_spline">b_spline</option>
-      <option value="interpolated">interpolated</option>
-    </param>
-    <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
-    <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
-      <option value="linear">linear</option>
-      <option value="cspline">cspline</option>
-      <option value="akima">akima</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="idXML">
-      <change_format>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
-      </change_format>
-    </data>
-    <data name="param_trafo_out" label="Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Corrects retention time distortions between maps based on common peptide identifications.
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="Input files to align (all must have the same file type)" 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 format="xml,consensusxml" help="(-file) " label="File to use as reference" name="param_reference_file" optional="True" type="data"/>
+      <param help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference" label="Use one of the input files as reference ('1' for the first file, etc.)" min="0" name="param_reference_index" optional="True" type="integer" value="0"/>
+      <param help="(-peptide_score_threshold) &lt;br&gt;Select a value that allows only 'high confidence' matches" label="Score threshold for peptide hits to be used in the alignment" name="param_algorithm_peptide_score_threshold" type="float" value="0.0"/>
+      <param help="(-min_run_occur) reference, if any) a peptide must occur in to be used for the alignment. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides" label="Minimum number of runs (incl" min="2" name="param_algorithm_min_run_occur" optional="True" type="integer" value="2"/>
+      <param help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. &lt;br&gt;If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale" label="Maximum realistic RT difference for a peptide (median per run vs" min="0.0" name="param_algorithm_max_rt_shift" optional="True" type="float" value="0.5"/>
+      <param checked="true" falsevalue="" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" name="param_algorithm_use_unassigned_peptides" optional="True" truevalue="-algorithm:use_unassigned_peptides" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. &lt;br&gt;Precludes 'use_unassigned_peptides'" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" name="param_algorithm_use_feature_rt" optional="True" truevalue="-algorithm:use_feature_rt" type="boolean"/>
+      <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="b_spline">
+        <option value="linear">linear</option>
+        <option value="b_spline">b_spline</option>
+        <option value="interpolated">interpolated</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Perform linear regression on 'y - x' vs" name="param_model_linear_symmetric_regression" optional="True" truevalue="-model:linear:symmetric_regression" type="boolean"/>
+      <param help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" min="0.0" name="param_model_b_spline_wavelength" optional="True" type="float" value="0.0"/>
+      <param help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing" label="Number of nodes for B-spline fitting" min="0" name="param_model_b_spline_num_nodes" optional="True" type="integer" value="5"/>
+      <param help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)" label="Method to use for extrapolation beyond the original data range" name="param_model_b_spline_extrapolate" optional="True" type="select" value="linear">
+        <option value="linear">linear</option>
+        <option value="b_spline">b_spline</option>
+        <option value="constant">constant</option>
+        <option value="global_linear">global_linear</option>
+      </param>
+      <param help="(-boundary_condition) " label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" max="2" min="0" name="param_model_b_spline_boundary_condition" optional="True" type="integer" value="2"/>
+      <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline">
+        <option value="linear">linear</option>
+        <option value="cspline">cspline</option>
+        <option value="akima">akima</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"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="input" metadata_source="param_in" name="param_out"/>
+      <data format="trafoxml" name="param_trafo_out"/>
+    </outputs>
+    <help>Corrects retention time distortions between maps based on common peptide identifications.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
+  </tool>