--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDMapper.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,97 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDMapper
+
+#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 $param_mz_measure:
+  -mz_measure
+  #if " " in str($param_mz_measure):
+    "$param_mz_measure"
+  #else
+    $param_mz_measure
+  #end if
+#end if
+#if $param_mz_reference:
+  -mz_reference
+  #if " " in str($param_mz_reference):
+    "$param_mz_reference"
+  #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,mzq" 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" help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <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" help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <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" 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.)">
+      <option value="precursor">precursor</option>
+      <option value="peptide">peptide</option>
+    </param>
+    <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge" falsevalue="" 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_feature_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt" falsevalue="" 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_feature_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz" falsevalue="" 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" 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.)"/>
+    <param name="param_consensus_use_subelements" type="boolean" truevalue="-consensus:use_subelements" falsevalue="" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="(-use_subelements) A consensus feature matches if any of its sub-features matches"/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_consensus_annotate_ids_with_subelements" type="boolean" truevalue="-consensus:annotate_ids_with_subelements" falsevalue="" checked="false" optional="True" label="Store the map index of the sub-feature in the peptide ID" help="(-annotate_ids_with_subelements) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" metadata_source="param_in" format="input"/>
+  </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</help>
+  <expand macro="references"/>
+</tool>