diff AccurateMassSearch.xml @ 12:4f9d07638178 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

--- a/AccurateMassSearch.xml	Mon Feb 12 09:02:12 2018 -0500
+++ b/AccurateMassSearch.xml	Wed May 15 06:58:08 2019 -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.-->
+<!--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: [Utilities]-->
-<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.2.0">
-  <description>Find potential HMDB ids within the given mass error window.</description>
+<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.3.0">
+  <description>Match MS signals to molecules from a database by mass.</description>
   <macros>
     <token name="@EXECUTABLE@">AccurateMassSearch</token>
     <import>macros.xml</import>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>AccurateMassSearch
+  <command detect_errors="aggressive"><![CDATA[AccurateMassSearch
 
 #if $param_in:
   -in $param_in
@@ -21,11 +21,11 @@
 #if $param_out_annotation:
   -out_annotation $param_out_annotation
 #end if
-#if $param_positive_adducts_file:
-  -positive_adducts_file $param_positive_adducts_file
+#if $param_positive_adducts:
+  -positive_adducts $param_positive_adducts
 #end if
-#if $param_negative_adducts_file:
-  -negative_adducts_file $param_negative_adducts_file
+#if $param_negative_adducts:
+  -negative_adducts $param_negative_adducts
 #end if
 -db:mapping
   #for token in $param_db_mapping:
@@ -68,11 +68,11 @@
   -force
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/>
-    <param name="param_positive_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
-    <param name="param_negative_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_positive_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_negative_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
     <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used">
       <sanitizer>
         <valid initial="string.printable">
@@ -110,8 +110,8 @@
     <data name="param_out" format="tabular"/>
     <data name="param_out_annotation" metadata_source="param_in" format="input"/>
   </outputs>
-  <help>Find potential HMDB ids within the given mass error window.
+  <help>Match MS signals to molecules from a database by mass.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_AccurateMassSearch.html</help>
 </tool>