diff RTEvaluation.xml @ 13:062fcf33f18d draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/RTEvaluation.xml	Fri Nov 06 20:12:48 2020 +0000
+++ b/RTEvaluation.xml	Thu Dec 01 19:21:02 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="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
   <macros>
     <token name="@EXECUTABLE@">RTEvaluation</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -49,15 +47,15 @@
     <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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
-    <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
-    <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/>
-    <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
-    <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/>
+    <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
+    <param argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
+    <param argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/>
+    <param argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
+    <param argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" 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">
@@ -70,13 +68,16 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_RTEvaluation"/>
-    <expand macro="manutest_RTEvaluation"/>
-  </tests>
+  <tests><!-- just chosen an arbitrary input and autgenerated output-->
+  <test expect_num_outputs="1">
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
+    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
+  </test>
+</tests>
   <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RTEvaluation.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RTEvaluation.html]]></help>
   <expand macro="references"/>
 </tool>