diff MascotAdapter.xml @ 1:36da1e3613ea draft

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

--- a/MascotAdapter.xml	Wed Mar 01 12:35:50 2017 -0500
+++ b/MascotAdapter.xml	Wed Aug 09 09:22:57 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: [Identification]-->
-<tool id="MascotAdapter" name="MascotAdapter" version="2.1.0">
+<tool id="MascotAdapter" name="MascotAdapter" version="2.2.0.1">
   <description>Annotates MS/MS spectra using Mascot.</description>
   <macros>
     <token name="@EXECUTABLE@">MascotAdapter</token>
@@ -34,7 +34,12 @@
   -peak_mass_tolerance $param_peak_mass_tolerance
 #end if
 #if $param_taxonomy:
-  -taxonomy $param_taxonomy
+  -taxonomy
+  #if " " in str($param_taxonomy):
+    "$param_taxonomy"
+  #else
+    $param_taxonomy
+  #end if
 #end if
 
 #if $rep_param_modifications:
@@ -76,7 +81,12 @@
   -hits     "$param_hits"
 #end if
 #if $param_cleavage:
-  -cleavage $param_cleavage
+  -cleavage
+  #if " " in str($param_cleavage):
+    "$param_cleavage"
+  #else
+    $param_cleavage
+  #end if
 #end if
 #if $param_missed_cleavages:
   -missed_cleavages $param_missed_cleavages
@@ -112,7 +122,12 @@
   -boundary     "$param_boundary"
 #end if
 #if $param_mass_type:
-  -mass_type $param_mass_type
+  -mass_type
+  #if " " in str($param_mass_type):
+    "$param_mass_type"
+  #else
+    $param_mass_type
+  #end if
 #end if
 #if $param_mascot_directory:
   -mascot_directory     "$param_mascot_directory"
@@ -127,7 +142,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="text" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
+    <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
     <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
     <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
     <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">