diff SpectraFilterParentPeakMower.xml @ 13:5694ec584f4c draft

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

--- a/SpectraFilterParentPeakMower.xml	Fri Nov 06 19:59:38 2020 +0000
+++ b/SpectraFilterParentPeakMower.xml	Thu Dec 01 19:06:48 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: [Identification]-->
-<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Applies thresholdfilter to peak spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,7 +39,7 @@
     <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="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
       <param name="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
       <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
@@ -53,9 +51,9 @@
       <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
     </section>
     <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">
@@ -68,13 +66,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SpectraFilterParentPeakMower"/>
-    <expand macro="manutest_SpectraFilterParentPeakMower"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+    <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
+  </test>
+</tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
   <expand macro="references"/>
 </tool>