--- a/IDMapper.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDMapper.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,59 +1,97 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDMapper" name="IDMapper" version="1.12.0">
-  <description>Assigns protein/peptide identifications to features or consensus features.</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDMapper</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDMapper
+<?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: [ID Processing]-->
+  <tool id="IDMapper" name="IDMapper" version="2.0.0">
+    <description>Assigns protein/peptide identifications to features or consensus features.</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDMapper</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDMapper
 
--id ${param_id}
--in ${param_in}
--out ${param_out}
--rt_tolerance ${param_rt_tolerance}
--mz_tolerance ${param_mz_tolerance}
--mz_measure ${param_mz_measure}
--mz_reference ${param_mz_reference}
-${param_ignore_charge}
--threads \${GALAXY_SLOTS:-24} 
-${param_use_centroid_rt}
-${param_use_centroid_mz}
-${param_use_subelements}
+#if $param_id:
+  -id $param_id
+#end if
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_rt_tolerance:
+  -rt_tolerance $param_rt_tolerance
+#end if
+#if $param_mz_tolerance:
+  -mz_tolerance $param_mz_tolerance
+#end if
+#if $param_mz_measure:
+  -mz_measure
+  #if &quot; &quot; in str($param_mz_measure):
+    &quot;$param_mz_measure&quot;
+  #else
+    $param_mz_measure
+  #end if
+#end if
+#if $param_mz_reference:
+  -mz_reference
+  #if &quot; &quot; in str($param_mz_reference):
+    &quot;$param_mz_reference&quot;
+  #else
+    $param_mz_reference
+  #end if
+#end if
+#if $param_ignore_charge:
+  -ignore_charge
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_feature_use_centroid_rt:
+  -feature:use_centroid_rt
+#end if
+#if $param_feature_use_centroid_mz:
+  -feature:use_centroid_mz
+#end if
+#if $param_consensus_use_subelements:
+  -consensus:use_subelements
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_consensus_annotate_ids_with_subelements:
+  -consensus:annotate_ids_with_subelements
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_id" type="data" format="idXML" optional="False" label="Protein/peptide identifications file" help="(-id)"/>
-    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Feature map/consensus map file" help="(-in)"/>
-    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-rt_tolerance)"/>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-mz_tolerance)"/>
-    <param name="param_mz_measure" type="select" optional="True" value="ppm" label="Unit of 'mz_tolerance'." help="(-mz_measure)">
-      <option value="ppm">ppm</option>
-      <option value="Da">Da</option>
-    </param>
-    <param name="param_mz_reference" type="select" optional="True" value="precursor" label="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" help="(-mz_reference)">
-      <option value="precursor">precursor</option>
-      <option value="peptide">peptide</option>
-    </param>
-    <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge true" falsevalue="-ignore_charge false" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." help="(-ignore_charge)"/>
-    <param name="param_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt true" falsevalue="-feature:use_centroid_rt false" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." help="(-use_centroid_rt)"/>
-    <param name="param_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz true" falsevalue="-feature:use_centroid_mz false" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" help="(-use_centroid_mz)"/>
-    <param name="param_use_subelements" type="boolean" truevalue="-consensus:use_subelements true" falsevalue="-consensus:use_subelements false" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." help="(-use_subelements)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file (the format depends on the input file format)." format="consensusXML">
-      <change_format>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-      </change_format>
-    </data>
-  </outputs>
-  <help>**What it does**
-
-Assigns protein/peptide identifications to features or consensus features.
+    <inputs>
+      <param format="xml,txt" help="(-id) " label="Protein/peptide identifications file" name="param_id" optional="False" type="data"/>
+      <param format="xml,consensusxml,mzq" help="(-in) " label="Feature map/consensus map file" name="param_in" optional="False" type="data"/>
+      <param help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_rt_tolerance" optional="True" type="float" value="5.0"/>
+      <param help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_mz_tolerance" optional="True" type="float" value="20.0"/>
+      <param help="(-mz_measure) " label="Unit of 'mz_tolerance'" name="param_mz_measure" optional="True" type="select" value="ppm">
+        <option value="ppm">ppm</option>
+        <option value="Da">Da</option>
+      </param>
+      <param help="(-mz_reference) If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', &lt;br&gt;masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. &lt;br&gt;('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" label="Source of m/z values for peptide identifications" name="param_mz_reference" optional="True" type="select" value="precursor">
+        <option value="precursor">precursor</option>
+        <option value="peptide">peptide</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-ignore_charge) " label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" name="param_ignore_charge" optional="True" truevalue="-ignore_charge" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-use_centroid_rt) " label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" name="param_feature_use_centroid_rt" optional="True" truevalue="-feature:use_centroid_rt" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-use_centroid_mz) &lt;br&gt;(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" name="param_feature_use_centroid_mz" optional="True" truevalue="-feature:use_centroid_mz" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-use_subelements) A consensus feature matches if any of its sub-features matches" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" name="param_consensus_use_subelements" optional="True" truevalue="-consensus:use_subelements" type="boolean"/>
+      <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="(-annotate_ids_with_subelements) " label="Store the map index of the sub-feature in the peptide ID" name="param_consensus_annotate_ids_with_subelements" optional="True" truevalue="-consensus:annotate_ids_with_subelements" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="input" metadata_source="param_in" name="param_out"/>
+    </outputs>
+    <help>Assigns protein/peptide identifications to features or consensus features.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help>
+  </tool>