diff IDScoreSwitcher.xml @ 13:4204882495f2 draft

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

--- a/IDScoreSwitcher.xml	Fri Nov 06 20:23:05 2020 +0000
+++ b/IDScoreSwitcher.xml	Thu Dec 01 19:20:22 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: [Utilities]-->
-<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Switches between different scores of peptide or protein hits in identification data</description>
   <macros>
     <token name="@EXECUTABLE@">IDScoreSwitcher</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,27 +39,26 @@
     <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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
-    <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
-    <param name="new_score" argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
+    <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
+    <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
+      <expand macro="list_string_san" name="new_score"/>
     </param>
-    <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
-      <option value="">default (nothing chosen)</option>
+    <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
       <option value="lower_better">lower_better</option>
       <option value="higher_better">higher_better</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="new_score_orientation"/>
     </param>
-    <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
+      <expand macro="list_string_san" name="new_score_type"/>
     </param>
-    <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
+      <expand macro="list_string_san" name="old_score"/>
     </param>
     <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">
@@ -74,13 +71,50 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_IDScoreSwitcher"/>
-    <expand macro="manutest_IDScoreSwitcher"/>
+  <tests><!-- UTILS_IDScoreSwitcher_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="IDFileConverter_12_output.idXML"/>
+      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="proteins" value="false"/>
+      <param name="new_score" value="Percolator_PEP"/>
+      <param name="new_score_orientation" value="lower_better"/>
+      <param name="new_score_type" value="Posterior Error Probability"/>
+      <param name="old_score" value="Percolator_qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_IDScoreSwitcher_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="IDScoreSwitcher_2_input.idXML"/>
+      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="proteins" value="true"/>
+      <param name="new_score" value="Posterior Probability_score"/>
+      <param name="new_score_orientation" value="higher_better"/>
+      <param name="new_score_type" value="Posterior Probability"/>
+      <param name="old_score" value=""/>
+      <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[Switches between different scores of peptide or protein hits in identification data
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDScoreSwitcher.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDScoreSwitcher.html]]></help>
   <expand macro="references"/>
 </tool>