diff FileConverter.xml @ 7:1fe84d73c19c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

--- a/FileConverter.xml	Thu Jan 11 18:06:14 2018 -0500
+++ b/FileConverter.xml	Mon Feb 12 13:06:03 2018 -0500
@@ -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.-->
+<!--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: [File Handling]-->
-<tool id="FileConverter" name="FileConverter" version="2.2.0">
+<tool id="FileConverter" name="FileConverter" version="2.3.0">
   <description>Converts between different MS file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">FileConverter</token>
@@ -44,6 +44,9 @@
     #if $adv_opts.param_force_MaxQuant_compatibility:
   -force_MaxQuant_compatibility
 #end if
+    #if $adv_opts.param_force_TPP_compatibility:
+  -force_TPP_compatibility
+#end if
     #if $adv_opts.param_write_scan_index:
   -write_scan_index
   #if " " in str($adv_opts.param_write_scan_index):
@@ -89,6 +92,7 @@
       <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_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_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>