diff SpecLibCreator.xml @ 13:da1fa8ce2d96 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:07:29 +0000
parents 5d837ca93d0e
children
line wrap: on
line diff
--- a/SpecLibCreator.xml	Fri Nov 06 20:24:10 2020 +0000
+++ b/SpecLibCreator.xml	Thu Dec 01 19:07:29 2022 +0000
@@ -1,13 +1,11 @@
 <?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 CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Creates an MSP formatted spectral library.</description>
   <macros>
     <token name="@EXECUTABLE@">SpecLibCreator</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -45,16 +43,16 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="info" argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
-    <param name="itemseperator" argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help="">
-      <expand macro="list_string_san"/>
+    <param argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
+    <param argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help="">
+      <expand macro="list_string_san" name="itemseperator"/>
     </param>
-    <param name="itemenclosed" argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
-    <param name="spec" argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
+    <param argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
+    <param argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -67,13 +65,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SpecLibCreator"/>
-    <expand macro="manutest_SpecLibCreator"/>
-  </tests>
+  <tests><!--TODO could not find test data -->
+</tests>
   <help><![CDATA[Creates an MSP formatted spectral library.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpecLibCreator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpecLibCreator.html]]></help>
   <expand macro="references"/>
 </tool>