--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PSMFeatureExtractor.xml	Mon Feb 12 13:40:23 2018 -0500
@@ -0,0 +1,89 @@
+<?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 CTDConverter.-->
+<!--Proposed Tool Section: [Utilities]-->
+<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0">
+  <description>Computes extra features for each input PSM.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PSMFeatureExtractor
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+
+#if $rep_param_extra:
+-extra
+  #for token in $rep_param_extra:
+    #if " " in str(token):
+      "$token.param_extra"
+    #else
+      $token.param_extra
+    #end if
+  #end for
+#end if
+#if $param_multiple_search_engines:
+  -multiple_search_engines
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_skip_db_check:
+  -skip_db_check
+#end if
+    #if $adv_opts.param_concat:
+  -concat
+#end if
+    #if $adv_opts.param_impute:
+  -impute
+#end if
+    #if $adv_opts.param_limit_imputation:
+  -limit_imputation
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <repeat name="rep_param_extra" min="0" title="param_extra">
+      <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/>
+    <expand macro="advanced_options">
+      <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/>
+      <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/>
+      <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/>
+      <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/>
+      <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_out" metadata_source="param_in" format="input"/>
+  </outputs>
+  <help>Computes extra features for each input PSM.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PSMFeatureExtractor.html</help>
+</tool>