--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FileConverter.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,86 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FileConverter" name="FileConverter" version="1.12.0">
+  <description>Converts between different MS file formats.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FileConverter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FileConverter
+
+-in ${param_in}
+-in_type ${param_in_type}
+-UID_postprocessing ${param_UID_postprocessing}
+-out ${param_out}
+-out_type ${param_out_type}
+${param_write_mzML_index}
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    ${adv_opts.param_TIC_DTA2D}
+    ${adv_opts.param_MGF_compact}
+    ${adv_opts.param_process_lowmemory}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/>
+    <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content#br#" help="(-in_type)">
+      <option value="mzData">mzData</option>
+      <option value="mzXML">mzXML</option>
+      <option value="mzML">mzML</option>
+      <option value="dta">dta</option>
+      <option value="dta2d">dta2d</option>
+      <option value="mgf">mgf</option>
+      <option value="featureXML">featureXML</option>
+      <option value="consensusXML">consensusXML</option>
+      <option value="ms2">ms2</option>
+      <option value="fid">fid</option>
+      <option value="tsv">tsv</option>
+      <option value="peplist">peplist</option>
+      <option value="kroenik">kroenik</option>
+      <option value="edta">edta</option>
+    </param>
+    <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data.#br#'none' keeps current IDs even if invalid.#br#'ensure' keeps current IDs but reassigns invalid ones.#br#'reassign' assigns new unique IDs." help="(-UID_postprocessing)">
+      <option value="none">none</option>
+      <option value="ensure">ensure</option>
+      <option value="reassign">reassign</option>
+    </param>
+    <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." help="(-out_type)">
+      <option value="mzData">mzData</option>
+      <option value="mzXML">mzXML</option>
+      <option value="mzML">mzML</option>
+      <option value="dta2d">dta2d</option>
+      <option value="mgf">mgf</option>
+      <option value="featureXML">featureXML</option>
+      <option value="consensusXML">consensusXML</option>
+      <option value="edta">edta</option>
+      <option value="csv">csv</option>
+    </param>
+    <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index true" falsevalue="-write_mzML_index false" checked="false" optional="True" label="Whether to add an index to the file when writing mzML files" help="(-write_mzML_index)"/>
+    <expand macro="advanced_options">
+      <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D true" falsevalue="-TIC_DTA2D false" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions." help="(-TIC_DTA2D)"/>
+      <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact true" falsevalue="-MGF_compact false" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact)"/>
+      <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory true" falsevalue="-process_lowmemory false" checked="false" optional="True" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." help="(-process_lowmemory)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file" format="tabular">
+      <change_format>
+        <when input="param_out_type" value="mzXML" format="mzXML"/>
+        <when input="param_out_type" value="mzML" format="mzML"/>
+        <when input="param_out_type" value="mgf" format="mgf"/>
+        <when input="param_out_type" value="featureXML" format="featureXML"/>
+        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
+      </change_format>
+    </data>
+  </outputs>
+  <help>**What it does**
+
+Converts between different MS file formats.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html
+
+@REFERENCES@
+</help>
+</tool>