diff IsobaricAnalyzer.xml @ 1:125774c3e8aa draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/IsobaricAnalyzer.xml	Wed Mar 01 12:22:29 2017 -0500
+++ b/IsobaricAnalyzer.xml	Wed Aug 09 09:05:28 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>
@@ -13,7 +13,12 @@
   <command>IsobaricAnalyzer
 
 #if $param_type:
-  -type $param_type
+  -type
+  #if " " in str($param_type):
+    "$param_type"
+  #else
+    $param_type
+  #end if
 #end if
 #if $param_in:
   -in $param_in
@@ -25,7 +30,12 @@
   -id_pool     "$param_id_pool"
 #end if
 #if $param_extraction_select_activation:
-  -extraction:select_activation $param_extraction_select_activation
+  -extraction:select_activation
+  #if " " in str($param_extraction_select_activation):
+    "$param_extraction_select_activation"
+  #else
+    $param_extraction_select_activation
+  #end if
 #end if
 #if $param_extraction_reporter_mass_shift:
   -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
@@ -34,7 +44,12 @@
   -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
 #end if
 #if $param_extraction_keep_unannotated_precursor:
-  -extraction:keep_unannotated_precursor $param_extraction_keep_unannotated_precursor
+  -extraction:keep_unannotated_precursor
+  #if " " in str($param_extraction_keep_unannotated_precursor):
+    "$param_extraction_keep_unannotated_precursor"
+  #else
+    $param_extraction_keep_unannotated_precursor
+  #end if
 #end if
 #if $param_extraction_min_reporter_intensity:
   -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
@@ -110,7 +125,12 @@
   #end for
 #end if
 #if $param_quantification_isotope_correction:
-  -quantification:isotope_correction $param_quantification_isotope_correction
+  -quantification:isotope_correction
+  #if " " in str($param_quantification_isotope_correction):
+    "$param_quantification_isotope_correction"
+  #else
+    $param_quantification_isotope_correction
+  #end if
 #end if
 #if $param_quantification_normalization:
   -quantification:normalization
@@ -146,7 +166,12 @@
   -tmt10plex:channel_131_description     "$param_tmt10plex_channel_131_description"
 #end if
 #if $param_tmt10plex_reference_channel:
-  -tmt10plex:reference_channel $param_tmt10plex_reference_channel
+  -tmt10plex:reference_channel
+  #if " " in str($param_tmt10plex_reference_channel):
+    "$param_tmt10plex_reference_channel"
+  #else
+    $param_tmt10plex_reference_channel
+  #end if
 #end if
 
 #if $rep_param_tmt10plex_correction_matrix:
@@ -199,7 +224,12 @@
   -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
 #end if
     #if $adv_opts.param_extraction_purity_interpolation:
-  -extraction:purity_interpolation $adv_opts.param_extraction_purity_interpolation
+  -extraction:purity_interpolation
+  #if " " in str($adv_opts.param_extraction_purity_interpolation):
+    "$adv_opts.param_extraction_purity_interpolation"
+  #else
+    $adv_opts.param_extraction_purity_interpolation
+  #end if
 #end if
 #end if
 </command>
@@ -211,7 +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="'"/>
@@ -234,7 +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>