diff MetaboliteSpectralMatcher.xml @ 1:e9729ff6055e draft

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

--- a/MetaboliteSpectralMatcher.xml	Wed Mar 01 12:16:51 2017 -0500
+++ b/MetaboliteSpectralMatcher.xml	Wed Aug 09 08:59:15 2017 -0400
@@ -1,8 +1,8 @@
 <?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: [Utilities]-->
-<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.1.0">
-  <description>Find potential HMDB ids within the given mass error window.</description>
+<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.2.0">
+  <description>Perform a spectral library search.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
     <import>macros.xml</import>
@@ -15,6 +15,9 @@
 #if $param_in:
   -in $param_in
 #end if
+#if $param_database:
+  -database $param_database
+#end if
 #if $param_out:
   -out $param_out
 #end if
@@ -25,13 +28,28 @@
   -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
 #end if
 #if $param_algorithm_mass_error_unit:
-  -algorithm:mass_error_unit $param_algorithm_mass_error_unit
+  -algorithm:mass_error_unit
+  #if " " in str($param_algorithm_mass_error_unit):
+    "$param_algorithm_mass_error_unit"
+  #else
+    $param_algorithm_mass_error_unit
+  #end if
 #end if
 #if $param_algorithm_report_mode:
-  -algorithm:report_mode $param_algorithm_report_mode
+  -algorithm:report_mode
+  #if " " in str($param_algorithm_report_mode):
+    "$param_algorithm_report_mode"
+  #else
+    $param_algorithm_report_mode
+  #end if
 #end if
 #if $param_algorithm_ionization_mode:
-  -algorithm:ionization_mode $param_algorithm_ionization_mode
+  -algorithm:ionization_mode
+  #if " " in str($param_algorithm_ionization_mode):
+    "$param_algorithm_ionization_mode"
+  #else
+    $param_algorithm_ionization_mode
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -40,7 +58,8 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzml" optional="False" label="mzML file" help="(-in) "/>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Input spectra" help="(-in) "/>
+    <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/>
     <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
     <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
     <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
@@ -62,7 +81,7 @@
   <outputs>
     <data name="param_out" format="tabular"/>
   </outputs>
-  <help>Find potential HMDB ids within the given mass error window.
+  <help>Perform a spectral library search.
 
 
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help>