diff FeatureFinderMRM.xml @ 16:ccc041d26ee1 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- a/FeatureFinderMRM.xml	Thu Dec 01 18:58:07 2022 +0000
+++ b/FeatureFinderMRM.xml	Fri Jun 14 21:42:04 2024 +0000
@@ -1,8 +1,7 @@
-<?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@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects two-dimensional features in LC-MS data.</description>
+  <description>Detects two-dimensional features in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMRM</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,18 +38,18 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" 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=""/>
-      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" optional="true" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
+      <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" 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" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
+      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
       <param name="write_debug_files" argument="-algorithm:write_debug_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help=""/>
       <param name="resample_traces" argument="-algorithm:resample_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help=""/>
       <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 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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -64,14 +63,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderMRM_1 -->
+  <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"/>
+      <output name="out" value="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"/>
@@ -86,11 +86,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMRM.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMRM.html]]></help>
   <expand macro="references"/>
 </tool>