--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraSTSearchAdapter.xml	Wed Aug 09 09:11:13 2017 -0400
@@ -0,0 +1,100 @@
+<?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="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.2.0.1">
+  <description>Interface to the SEARCH Mode of the SpectraST executable</description>
+  <macros>
+    <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SpectraSTSearchAdapter
+
+-spectra_files
+  #for token in $param_spectra_files:
+    $token
+  #end for
+
+#if $rep_param_output_files:
+-output_files
+  #for token in $rep_param_output_files:
+    #if " " in str(token):
+      "$token.param_output_files"
+    #else
+      $token.param_output_files
+    #end if
+  #end for
+#end if
+#if $param_library_file:
+  -library_file $param_library_file
+#end if
+#if $param_sequence_database_file:
+  -sequence_database_file $param_sequence_database_file
+#end if
+#if $param_sequence_database_type:
+  -sequence_database_type
+  #if " " in str($param_sequence_database_type):
+    "$param_sequence_database_type"
+  #else
+    $param_sequence_database_type
+  #end if
+#end if
+#if $param_search_file:
+  -search_file $param_search_file
+#end if
+#if $param_params_file:
+  -params_file $param_params_file
+#end if
+#if $param_precursor_mz_tolerance:
+  -precursor_mz_tolerance $param_precursor_mz_tolerance
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_use_isotopically_averaged_mass:
+  -use_isotopically_averaged_mass
+#end if
+    #if $adv_opts.param_use_all_charge_states:
+  -use_all_charge_states
+#end if
+    #if $adv_opts.param_user_mod_file:
+  -user_mod_file $adv_opts.param_user_mod_file
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/>
+    <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/>
+    <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) ">
+      <option value="DNA">DNA</option>
+      <option value="AA" selected="true">AA</option>
+    </param>
+    <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/>
+    <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/>
+    <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/>
+    <expand macro="advanced_options">
+      <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/>
+      <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/>
+      <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/>
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_output_files" format="txt"/>
+  </outputs>
+  <help>Interface to the SEARCH Mode of the SpectraST executable
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpectraSTSearchAdapter.html</help>
+</tool>