Mercurial > repos > galaxyp > openms_highresprecursormasscorrector

diff HighResPrecursorMassCorrector.xml @ 15:d3546bb9fd8e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:01:37 +0000
parents cdbd06d8cbd5
children b606d4a12558
line wrap: on
line diff
--- a/HighResPrecursorMassCorrector.xml	Fri Nov 06 20:17:40 2020 +0000
+++ b/HighResPrecursorMassCorrector.xml	Thu Dec 01 19:01:37 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="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Corrects the precursor mass and charge determined by the instrument software.</description>
   <macros>
     <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -62,14 +60,14 @@
     <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 (centroided data)" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
     <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
       <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
       <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
-      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
       <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
       <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
@@ -79,24 +77,24 @@
     </section>
     <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
       <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
     </section>
     <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
       <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
     </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">
@@ -113,13 +111,207 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_HighResPrecursorMassCorrector"/>
-    <expand macro="manutest_HighResPrecursorMassCorrector"/>
+  <tests><!-- TOPP_HighResPrecursorMassCorrector_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="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
+        <param name="mz_tolerance" value="5.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="2"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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_HighResPrecursorMassCorrector_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="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
+        <param name="mz_tolerance" value="10.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="4"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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_HighResPrecursorMassCorrector_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
+        <param name="mz_tolerance" value="5.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="2"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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_HighResPrecursorMassCorrector_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
+        <param name="mz_tolerance" value="5.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="2"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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_HighResPrecursorMassCorrector_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
+        <param name="mz_tolerance" value="5.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="2"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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_HighResPrecursorMassCorrector_6 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
+      <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="feature">
+        <param name="mz_tolerance" value="5.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+        <param name="rt_tolerance" value="0.0"/>
+        <param name="max_trace" value="2"/>
+        <param name="believe_charge" value="false"/>
+        <param name="keep_original" value="false"/>
+        <param name="assign_all_matching" value="false"/>
+      </section>
+      <section name="nearest_peak">
+        <param name="mz_tolerance" value="0.0"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </section>
+      <section name="highest_intensity_peak">
+        <param name="mz_tolerance" value="0.2"/>
+        <param name="mz_tolerance_unit" value="ppm"/>
+      </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[Corrects the precursor mass and charge determined by the instrument software.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
   <expand macro="references"/>
 </tool>