--- a/AccurateMassSearch.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/AccurateMassSearch.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,66 +1,102 @@
-<?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
+<?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: [Utilities]-->
+  <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0">
+    <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="references"/>
+    <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}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_annotation:
+  -out_annotation $param_out_annotation
+#end if
+#if $param_positive_adducts_file:
+  -positive_adducts_file $param_positive_adducts_file
+#end if
+#if $param_negative_adducts_file:
+  -negative_adducts_file $param_negative_adducts_file
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_db_mapping:
+  -db:mapping $param_db_mapping
+#end if
+#if $param_db_struct:
+  -db:struct $param_db_struct
+#end if
+#if $param_algorithm_mass_error_value:
+  -algorithm:mass_error_value $param_algorithm_mass_error_value
+#end if
+#if $param_algorithm_mass_error_unit:
+  -algorithm:mass_error_unit
+  #if &quot; &quot; in str($param_algorithm_mass_error_unit):
+    &quot;$param_algorithm_mass_error_unit&quot;
+  #else
+    $param_algorithm_mass_error_unit
+  #end if
+#end if
+#if $param_algorithm_ionization_mode:
+  -algorithm:ionization_mode
+  #if &quot; &quot; in str($param_algorithm_ionization_mode):
+    &quot;$param_algorithm_ionization_mode&quot;
+  #else
+    $param_algorithm_ionization_mode
+  #end if
+#end if
+#if $param_algorithm_isotopic_similarity:
+  -algorithm:isotopic_similarity
+#end if
+#if $param_algorithm_keep_unidentified_masses:
+  -algorithm:keep_unidentified_masses
+#end if
+#if $param_algorithm_mzTab_exportIsotopeIntensities:
+  -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities
+#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" 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.
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="featureXML or consensusXML file" name="param_in" optional="False" type="data"/>
+      <param format="tabular" help="(-positive_adducts_file) 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" label="This file contains the list of potential positive adducts that will be looked for in the database" name="param_positive_adducts_file" optional="False" type="data" value="CHEMISTRY/PositiveAdducts.tsv"/>
+      <param format="tabular" help="(-negative_adducts_file) 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" label="This file contains the list of potential negative adducts that will be looked for in the database" name="param_negative_adducts_file" optional="False" type="data" value="CHEMISTRY/NegativeAdducts.tsv"/>
+      <param format="tabular" help="(-mapping) 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" label="Database input file, containing three tab-separated columns of mass, formula, identifie" name="param_db_mapping" optional="False" type="data" value="CHEMISTRY/HMDBMappingFile.tsv"/>
+      <param format="tabular" help="(-struct) 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" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" name="param_db_struct" optional="False" type="data" value="CHEMISTRY/HMDB2StructMapping.tsv"/>
+      <param help="(-mass_error_value) " label="Tolerance allowed for accurate mass search" name="param_algorithm_mass_error_value" type="float" value="5.0"/>
+      <param help="(-mass_error_unit) " label="Unit of mass error (ppm or Da)" name="param_algorithm_mass_error_unit" optional="True" type="select" value="ppm">
+        <option value="ppm">ppm</option>
+        <option value="Da">Da</option>
+      </param>
+      <param help="(-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" label="Positive or negative ionization mode?" name="param_algorithm_ionization_mode" optional="True" type="select" value="positive">
+        <option value="positive">positive</option>
+        <option value="negative">negative</option>
+        <option value="auto">auto</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-isotopic_similarity) " label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" name="param_algorithm_isotopic_similarity" optional="True" truevalue="-algorithm:isotopic_similarity" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-keep_unidentified_masses) " label="Keep features that did not yield any DB hit" name="param_algorithm_keep_unidentified_masses" optional="True" truevalue="-algorithm:keep_unidentified_masses" type="boolean"/>
+      <param help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" min="0" name="param_algorithm_mzTab_exportIsotopeIntensities" optional="True" type="integer" value="0"/>
+      <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="tabular" name="param_out"/>
+      <data format="input" metadata_source="param_in" name="param_out_annotation"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
+  </tool>