--- a/InternalCalibration.xml	Wed Mar 01 12:37:28 2017 -0500
+++ b/InternalCalibration.xml	Wed Aug 09 09:25:50 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: [Signal processing and preprocessing]-->
-<tool id="InternalCalibration" name="InternalCalibration" version="2.1.0">
+<tool id="InternalCalibration" name="InternalCalibration" version="2.2.0.1">
   <description>Applies an internal mass recalibration.</description>
   <macros>
     <token name="@EXECUTABLE@">InternalCalibration</token>
@@ -57,7 +57,12 @@
   -cal:lock_require_iso
 #end if
 #if $param_cal_model_type:
-  -cal:model_type $param_cal_model_type
+  -cal:model_type
+  #if " " in str($param_cal_model_type):
+    "$param_cal_model_type"
+  #else
+    $param_cal_model_type
+  #end if
 #end if
 #if $param_RANSAC_enabled:
   -RANSAC:enabled
@@ -97,7 +102,7 @@
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
-    <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
+    <param name="param_rscript_executable" type="data" format="txt" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
     <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/>
     <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
       <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection">
@@ -110,7 +115,7 @@
       </param>
     </repeat>
     <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
-    <param name="param_cal_id_in" type="data" format="featurexml,idxml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/>
+    <param name="param_cal_id_in" type="data" format="idxml,featurexml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/>
     <param name="param_cal_lock_in" type="data" format="tabular" optional="True" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help="(-lock_in) "/>
     <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
     <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/>