diff PeakPickerIterative.xml @ 13:9547baeca6a1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:59:31 +0000
parents 0c37d0660a6b
children 025261d4bd60
line wrap: on
line diff
--- a/PeakPickerIterative.xml	Fri Nov 06 20:14:18 2020 +0000
+++ b/PeakPickerIterative.xml	Thu Dec 01 18:59:31 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="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Finds mass spectrometric peaks in profile mass spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerIterative</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 parameters section" help="" expanded="false">
       <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
       <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
@@ -54,9 +52,9 @@
       <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" 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">
@@ -69,13 +67,62 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_PeakPickerIterative"/>
-    <expand macro="manutest_PeakPickerIterative"/>
+  <tests><!-- UTILS_PeakPickerIterative_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="PeakPickerIterative_1_input.mzML"/>
+      <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="signal_to_noise_" value="1.0"/>
+        <param name="peak_width" value="0.04"/>
+        <param name="spacing_difference" value="1.5"/>
+        <param name="sn_bin_count_" value="30"/>
+        <param name="nr_iterations_" value="5"/>
+        <param name="sn_win_len_" value="20.0"/>
+        <param name="check_width_internally" value="false"/>
+        <param name="ms1_only" value="false"/>
+        <param name="clear_meta_data" 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>
+    <!-- UTILS_PeakPickerIterative_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="PeakPickerIterative_2_input.mzML"/>
+      <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="signal_to_noise_" value="0.0"/>
+        <param name="peak_width" value="0.04"/>
+        <param name="spacing_difference" value="2.5"/>
+        <param name="sn_bin_count_" value="30"/>
+        <param name="nr_iterations_" value="5"/>
+        <param name="sn_win_len_" value="20.0"/>
+        <param name="check_width_internally" value="true"/>
+        <param name="ms1_only" value="false"/>
+        <param name="clear_meta_data" 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[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_PeakPickerIterative.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PeakPickerIterative.html]]></help>
   <expand macro="references"/>
 </tool>