diff OpenSwathConfidenceScoring.xml @ 13:c1809c05ae8c draft

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

--- a/OpenSwathConfidenceScoring.xml	Fri Nov 06 20:04:09 2020 +0000
+++ b/OpenSwathConfidenceScoring.xml	Thu Dec 01 19:01:26 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: [Targeted Experiments]-->
-<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Compute confidence scores for OpenSwath results</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -53,20 +51,20 @@
     <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="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
-    <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
-    <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
-    <param name="decoys" argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
-    <param name="transitions" argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
+    <param argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
+    <param argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
+    <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
+    <param argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
+    <param argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
     <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
       <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
       <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
       <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" 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">
@@ -79,13 +77,34 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_OpenSwathConfidenceScoring"/>
-    <expand macro="manutest_OpenSwathConfidenceScoring"/>
+  <tests><!-- TOPP_OpenSwathConfidenceScoring_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="OpenSwathFeatureXMLToTSV_input.featureXML"/>
+      <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
+      <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
+      <param name="decoys" value="1"/>
+      <param name="transitions" value="2"/>
+      <section name="GLM">
+        <param name="intercept" value="3.87333466"/>
+        <param name="delta_rt" value="-0.02898629"/>
+        <param name="dist_int" value="-7.75880768"/>
+      </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[Compute confidence scores for OpenSwath results
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
   <expand macro="references"/>
 </tool>