Mercurial > repos > galaxyp > openms_labeledeval

diff LabeledEval.xml @ 13:45b7070b3366 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:25:01 +0000
parents 01d8dbc6ccf7
children
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--- a/LabeledEval.xml	Fri Nov 06 20:35:17 2020 +0000
+++ b/LabeledEval.xml	Thu Dec 01 19:25:01 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="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
   <macros>
     <token name="@EXECUTABLE@">LabeledEval</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -42,14 +40,14 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
-    <param name="truth" argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
-    <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
-    <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
+    <param argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
+    <param argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
+    <param argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
+    <param argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
     <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">
@@ -64,13 +62,16 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_LabeledEval"/>
-    <expand macro="manutest_LabeledEval"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
+    <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
+    <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
+  </test>
+</tests>
   <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_LabeledEval.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_LabeledEval.html]]></help>
   <expand macro="references"/>
 </tool>