--- a/FileConverter.xml	Thu Apr 27 13:21:34 2017 -0400
+++ b/FileConverter.xml	Wed Aug 09 09:42:16 2017 -0400
@@ -1,7 +1,7 @@
 <?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: [File Handling]-->
-<tool id="FileConverter" name="FileConverter" version="2.1.0">
+<tool id="FileConverter" name="FileConverter" version="2.2.0">
   <description>Converts between different MS file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">FileConverter</token>
@@ -15,35 +15,49 @@
 #if $param_in:
   -in $param_in
 #end if
-#if $param_UID_postprocessing:
-  -UID_postprocessing
-  #if " " in str($param_UID_postprocessing):
-    "$param_UID_postprocessing"
-  #else
-    $param_UID_postprocessing
-  #end if
-#end if
 #if $param_out:
   -out $param_out
 #end if
-#if $param_out_type:
-  -out_type
-  #if " " in str($param_out_type):
-    "$param_out_type"
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_UID_postprocessing:
+  -UID_postprocessing
+  #if " " in str($adv_opts.param_UID_postprocessing):
+    "$adv_opts.param_UID_postprocessing"
   #else
-    $param_out_type
+    $adv_opts.param_UID_postprocessing
   #end if
 #end if
-#if $param_write_mzML_index:
-  -write_mzML_index
+    #if $adv_opts.param_out_type:
+  -out_type
+  #if " " in str($adv_opts.param_out_type):
+    "$adv_opts.param_out_type"
+  #else
+    $adv_opts.param_out_type
+  #end if
 #end if
-#if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_TIC_DTA2D:
   -TIC_DTA2D
 #end if
     #if $adv_opts.param_MGF_compact:
   -MGF_compact
 #end if
+    #if $adv_opts.param_force_MaxQuant_compatibility:
+  -force_MaxQuant_compatibility
+#end if
+    #if $adv_opts.param_write_scan_index:
+  -write_scan_index
+  #if " " in str($adv_opts.param_write_scan_index):
+    "$adv_opts.param_write_scan_index"
+  #else
+    $adv_opts.param_write_scan_index
+  #end if
+#end if
+    #if $adv_opts.param_lossy_compression:
+  -lossy_compression
+#end if
+    #if $adv_opts.param_lossy_mass_accuracy:
+  -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy
+#end if
     #if $adv_opts.param_process_lowmemory:
   -process_lowmemory
 #end if
@@ -53,28 +67,34 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
-    <param name="param_UID_postprocessing" display="radio" type="select" optional="False" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs">
-      <option value="none">none</option>
-      <option value="ensure" selected="true">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 &lt;br&gt;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="cachedMzML">cachedMzML</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" display="radio" type="boolean" truevalue="-write_mzML_index" falsevalue="" checked="false" optional="True" label="Add an index to the file when writing mzML files (default: no index)" help="(-write_mzML_index) "/>
+    <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
     <expand macro="advanced_options">
+      <param name="param_UID_postprocessing" display="radio" type="select" optional="False" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs">
+        <option value="none">none</option>
+        <option value="ensure" selected="true">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 &lt;br&gt;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="cachedMzML">cachedMzML</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_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" 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" display="radio" type="boolean" truevalue="-MGF_compact" falsevalue="" 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_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
+      <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/>
+      <param name="param_lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression (" help="(-lossy_mass_accuracy) e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
       <param name="param_process_lowmemory" display="radio" type="boolean" truevalue="-process_lowmemory" falsevalue="" 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)" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms"/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
     </expand>