--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMapper.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+<?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
+
+-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}
+</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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html
+
+@REFERENCES@
+</help>
+</tool>