--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AccurateMassSearch.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,66 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="AccurateMassSearch" name="AccurateMassSearch" version="1.12.0">
+  <description>Find potential HMDB ids within the given mass error window.</description>
+  <macros>
+    <token name="@EXECUTABLE@">AccurateMassSearch</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>AccurateMassSearch
+
+-in ${param_in}
+-out ${param_out}
+-out_annotation ${param_out_annotation}
+-positive_adducts_file ${param_positive_adducts_file}
+-negative_adducts_file ${param_negative_adducts_file}
+-threads \${GALAXY_SLOTS:-24} 
+-db:mapping ${param_mapping}
+-db:struct ${param_struct}
+-algorithm:mass_error_value ${param_mass_error_value}
+-algorithm:mass_error_unit ${param_mass_error_unit}
+-algorithm:ionization_mode ${param_ionization_mode}
+${param_isotopic_similarity}
+-algorithm:report_mode ${param_report_mode}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="featureXML or consensusXML file" help="(-in)"/>
+    <param name="param_positive_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used." help="(-positive_adducts_file)"/>
+    <param name="param_negative_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used." help="(-negative_adducts_file)"/>
+    <param name="param_mapping" type="data" format="" optional="False" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file, containing three tab-separated columns of mass, formula, identifier. If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used." help="(-mapping)"/>
+    <param name="param_struct" type="data" format="" optional="False" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file. SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used." help="(-struct)"/>
+    <param name="param_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search." help="(-mass_error_value)"/>
+    <param name="param_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit)">
+      <option value="ppm">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_ionization_mode" type="select" optional="True" value="positive" label="Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error." help="(-ionization_mode)">
+      <option value="positive">positive</option>
+      <option value="negative">negative</option>
+      <option value="auto">auto</option>
+    </param>
+    <param name="param_isotopic_similarity" type="boolean" truevalue="-algorithm:isotopic_similarity true" falsevalue="-algorithm:isotopic_similarity false" checked="false" optional="True" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)." help="(-isotopic_similarity)"/>
+    <param name="param_report_mode" type="select" optional="True" value="all" label="Results are reported in one of several modes: Either (all) matching hits, the (top3) scoring hits, or the (best) scoring hit." help="(-report_mode)">
+      <option value="all">all</option>
+      <option value="top3">top3</option>
+      <option value="best">best</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="mzTab file" format="tabular"/>
+    <data name="param_out_annotation" label="The input file, annotated with matching hits from the database." format="consensusXML">
+      <change_format>
+        <when input="param_out_type" value="featureXML" format="featureXML"/>
+      </change_format>
+    </data>
+  </outputs>
+  <help>**What it does**
+
+Find potential HMDB ids within the given mass error window.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html
+
+@REFERENCES@
+</help>
+</tool>