diff NoiseFilterSGolay.xml @ 13:cf86c9091cb3 draft

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

--- a/NoiseFilterSGolay.xml	Fri Nov 06 19:44:17 2020 +0000
+++ b/NoiseFilterSGolay.xml	Thu Dec 01 19:05:55 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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
   <macros>
     <token name="@EXECUTABLE@">NoiseFilterSGolay</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,20 +39,20 @@
     <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 raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
       <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="processOption"/>
       </param>
-      <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">
@@ -67,13 +65,90 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_NoiseFilterSGolay"/>
-    <expand macro="manutest_NoiseFilterSGolay"/>
+  <tests><!-- TOPP_NoiseFilterSGolay_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="inmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
+      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="frame_length" value="9"/>
+        <param name="polynomial_order" value="4"/>
+      </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_NoiseFilterSGolay_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="inmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
+      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="frame_length" value="11"/>
+        <param name="polynomial_order" value="4"/>
+      </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_NoiseFilterSGolay_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="lowmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
+      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="frame_length" value="9"/>
+        <param name="polynomial_order" value="4"/>
+      </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_NoiseFilterSGolay_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="processOption" value="lowmemory"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
+      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="frame_length" value="11"/>
+        <param name="polynomial_order" value="4"/>
+      </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[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_NoiseFilterSGolay.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help>
   <expand macro="references"/>
 </tool>