diff FeatureFinderMRM.xml @ 15:646ebe78d904 draft

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

--- a/FeatureFinderMRM.xml	Fri Nov 06 19:45:45 2020 +0000
+++ b/FeatureFinderMRM.xml	Thu Dec 01 18:58:07 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: [Quantitation]-->
-<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Detects two-dimensional features in LC-MS data.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMRM</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 section" help="" expanded="false">
       <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" optional="true" min="0.0" value="10.0" label="Minimal distance of MRM features in seconds" help=""/>
       <param name="min_num_peaks_per_feature" argument="-algorithm:min_num_peaks_per_feature" type="integer" optional="true" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
@@ -51,9 +49,9 @@
       <param name="write_debuginfo" argument="-algorithm:write_debuginfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, debug messages are written, the output can be somewhat lengthy" 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">
@@ -66,13 +64,33 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_FeatureFinderMRM"/>
-    <expand macro="manutest_FeatureFinderMRM"/>
+  <tests><!-- TOPP_FeatureFinderMRM_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
+      <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <section name="algorithm">
+        <param name="min_rt_distance" value="10.0"/>
+        <param name="min_num_peaks_per_feature" value="5"/>
+        <param name="min_signal_to_noise_ratio" value="2.0"/>
+        <param name="write_debug_files" value="false"/>
+        <param name="resample_traces" value="false"/>
+        <param name="write_debuginfo" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMRM.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMRM.html]]></help>
   <expand macro="references"/>
 </tool>