diff MassTraceExtractor.xml @ 13:29d893e855c6 draft

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

--- a/MassTraceExtractor.xml	Fri Nov 06 20:38:37 2020 +0000
+++ b/MassTraceExtractor.xml	Thu Dec 01 19:00:15 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: [Signal processing and preprocessing]-->
-<tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Detects mass traces in centroided LC-MS data.</description>
   <macros>
     <token name="@EXECUTABLE@">MassTraceExtractor</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,11 +39,11 @@
     <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 centroided mzML file" help=" select mzml data sets(s)"/>
-    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mzml" optional="false" label="input centroided mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="out_type"/>
     </param>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <section name="common" title="" help="" expanded="false">
@@ -56,16 +54,16 @@
       <section name="mtd" title="" help="" expanded="false">
         <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="trace_termination_criterion"/>
         </param>
         <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
         <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
@@ -73,11 +71,11 @@
         <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
       </section>
       <section name="epd" title="" help="" expanded="false">
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="width_filtering"/>
         </param>
         <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
         <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
@@ -86,9 +84,9 @@
       </section>
     </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">
@@ -96,9 +94,8 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
       <change_format>
-        <when input="out_type" value="consensusXML" format="consensusxml"/>
         <when input="out_type" value="featureXML" format="featurexml"/>
       </change_format>
     </data>
@@ -106,13 +103,90 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MassTraceExtractor"/>
-    <expand macro="manutest_MassTraceExtractor"/>
+  <tests><!-- TOPP_MassTraceExtractor_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="MassTraceExtractor_1_input.mzML"/>
+      <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <param name="out_type" value="featureXML"/>
+      <section name="algorithm">
+        <section name="common">
+          <param name="noise_threshold_int" value="10.0"/>
+          <param name="chrom_peak_snr" value="3.0"/>
+          <param name="chrom_fwhm" value="5.0"/>
+        </section>
+        <section name="mtd">
+          <param name="mass_error_ppm" value="20.0"/>
+          <param name="reestimate_mt_sd" value="true"/>
+          <param name="quant_method" value="area"/>
+          <param name="trace_termination_criterion" value="outlier"/>
+          <param name="trace_termination_outliers" value="5"/>
+          <param name="min_sample_rate" value="0.5"/>
+          <param name="min_trace_length" value="5.0"/>
+          <param name="max_trace_length" value="-1.0"/>
+        </section>
+        <section name="epd">
+          <param name="width_filtering" value="off"/>
+          <param name="min_fwhm" value="3.0"/>
+          <param name="max_fwhm" value="60.0"/>
+          <param name="masstrace_snr_filtering" value="false"/>
+          <param name="enabled" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MassTraceExtractor_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MassTraceExtractor_1_input.mzML"/>
+      <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <param name="out_type" value="featureXML"/>
+      <section name="algorithm">
+        <section name="common">
+          <param name="noise_threshold_int" value="10.0"/>
+          <param name="chrom_peak_snr" value="3.0"/>
+          <param name="chrom_fwhm" value="5.0"/>
+        </section>
+        <section name="mtd">
+          <param name="mass_error_ppm" value="20.0"/>
+          <param name="reestimate_mt_sd" value="true"/>
+          <param name="quant_method" value="area"/>
+          <param name="trace_termination_criterion" value="outlier"/>
+          <param name="trace_termination_outliers" value="5"/>
+          <param name="min_sample_rate" value="0.5"/>
+          <param name="min_trace_length" value="6.0"/>
+          <param name="max_trace_length" value="12.0"/>
+        </section>
+        <section name="epd">
+          <param name="width_filtering" value="off"/>
+          <param name="min_fwhm" value="3.0"/>
+          <param name="max_fwhm" value="60.0"/>
+          <param name="masstrace_snr_filtering" value="false"/>
+          <param name="enabled" value="true"/>
+        </section>
+      </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 mass traces in centroided LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MassTraceExtractor.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MassTraceExtractor.html]]></help>
   <expand macro="references"/>
 </tool>