diff IsobaricAnalyzer.xml @ 4:bec6abb425bf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

--- a/IsobaricAnalyzer.xml	Thu Apr 27 12:56:04 2017 -0400
+++ b/IsobaricAnalyzer.xml	Fri Jul 14 18:53:23 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: [Quantitation]-->
-<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.1.0">
+<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0">
   <description>Calculates isobaric quantitative values for peptides</description>
   <macros>
     <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
@@ -241,7 +241,7 @@
       <option value="tmt6plex">tmt6plex</option>
     </param>
     <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
-    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)">
+    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -264,7 +264,7 @@
       <option value="Electron transfer dissociation">Electron transfer dissociation</option>
       <option value=""></option>
     </param>
-    <param name="param_extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/>
+    <param name="param_extraction_reporter_mass_shift" type="float" min="0.0001" max="0.5" optional="True" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help="(-reporter_mass_shift) "/>
     <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
     <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) ">
       <option value="true" selected="true">true</option>