diff ClusterMassTraces.xml @ 4:10c41ad01df5 draft default tip

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

--- a/ClusterMassTraces.xml	Fri Nov 06 20:04:54 2020 +0000
+++ b/ClusterMassTraces.xml	Thu Dec 01 19:11:57 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="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Creates pseudo spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">ClusterMassTraces</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,17 +39,17 @@
     <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="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
-    <param name="min_pearson_correlation" argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
-    <param name="min_peak_nr" argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
-    <param name="max_lag" argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
-    <param name="max_rt_apex_difference" argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
-    <param name="max_intensity_cutoff" argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
-    <param name="add_precursor" argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
+    <param argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
+    <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
+    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
+    <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
+    <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" 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 +62,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_ClusterMassTraces"/>
-    <expand macro="manutest_ClusterMassTraces"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+    <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
+  </test>
+</tests>
   <help><![CDATA[Creates pseudo spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ClusterMassTraces.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTraces.html]]></help>
   <expand macro="references"/>
 </tool>