--- a/FileFilter.xml	Thu Apr 27 13:21:46 2017 -0400
+++ b/FileFilter.xml	Wed Aug 09 09:52:35 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="FileFilter" name="FileFilter" version="2.1.0">
+<tool id="FileFilter" name="FileFilter" version="2.2.0">
   <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
   <macros>
     <token name="@EXECUTABLE@">FileFilter</token>
@@ -105,6 +105,9 @@
 #if $param_peak_options_indexed_file:
   -peak_options:indexed_file
 #end if
+#if $param_peak_options_zlib_compression:
+  -peak_options:zlib_compression
+#end if
 #if $param_peak_options_numpress_masstime:
   -peak_options:numpress:masstime
   #if " " in str($param_peak_options_numpress_masstime):
@@ -338,7 +341,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/>
+    <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/>
     <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) ">
       <option value="mzML">mzML</option>
       <option value="featureXML">featureXML</option>
@@ -420,20 +423,21 @@
       <option value="64">64</option>
     </param>
     <param name="param_peak_options_indexed_file" display="radio" type="boolean" truevalue="-peak_options:indexed_file" falsevalue="" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file) "/>
+    <param name="param_peak_options_zlib_compression" display="radio" type="boolean" truevalue="-peak_options:zlib_compression" falsevalue="" checked="false" optional="True" label="Whether to store data with zlib compression (lossless compression)" help="(-zlib_compression) "/>
     <param name="param_peak_options_numpress_masstime" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) ">
       <option value="none" selected="true">none</option>
       <option value="linear">linear</option>
       <option value="pic">pic</option>
       <option value="slof">slof</option>
     </param>
-    <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" help="(-masstime_error) "/>
+    <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (default 10 ppm at 100 m/z; set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-masstime_error) "/>
     <param name="param_peak_options_numpress_intensity" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) ">
       <option value="none" selected="true">none</option>
       <option value="linear">linear</option>
       <option value="pic">pic</option>
       <option value="slof">slof</option>
     </param>
-    <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic)" help="(-intensity_error) "/>
+    <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-intensity_error) "/>
     <param name="param_spectra_remove_zoom" display="radio" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/>
     <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) ">
       <option value="Unknown">Unknown</option>