diff TICCalculator.xml @ 13:d623ad21ca59 draft

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

--- a/TICCalculator.xml	Fri Nov 06 20:36:04 2020 +0000
+++ b/TICCalculator.xml	Thu Dec 01 19:10:31 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: [Utilities]-->
-<tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
   <macros>
     <token name="@EXECUTABLE@">TICCalculator</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -38,21 +36,21 @@
     <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="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
-    <param name="read_method" argument="-read_method" type="select" optional="false" label="Method to read the file" help="">
+    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
+    <param argument="-read_method" type="select" optional="true" label="Method to read the file" help="">
       <option value="regular" selected="true">regular</option>
       <option value="indexed">indexed</option>
       <option value="indexed_parallel">indexed_parallel</option>
       <option value="streaming">streaming</option>
       <option value="cached">cached</option>
       <option value="cached_parallel">cached_parallel</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="read_method"/>
     </param>
-    <param name="loadData" argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/>
+    <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/>
     <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">
@@ -67,13 +65,90 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_TICCalculator"/>
-    <expand macro="manutest_TICCalculator"/>
+  <tests><!-- UTILS_TICCalculator_1 -->
+    <test expect_num_outputs="1">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MapNormalizer_output.mzML"/>
+      <param name="read_method" value="regular"/>
+      <param name="loadData" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_TICCalculator_2 -->
+    <test expect_num_outputs="1">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MapNormalizer_output.mzML"/>
+      <param name="read_method" value="streaming"/>
+      <param name="loadData" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_TICCalculator_3 -->
+    <test expect_num_outputs="1">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MapNormalizer_output.mzML"/>
+      <param name="read_method" value="streaming"/>
+      <param name="loadData" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_TICCalculator_4 -->
+    <test expect_num_outputs="1">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MapNormalizer_output.mzML"/>
+      <param name="read_method" value="indexed"/>
+      <param name="loadData" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_TICCalculator_5 -->
+    <test expect_num_outputs="1">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MapNormalizer_output.mzML"/>
+      <param name="read_method" value="indexed_parallel"/>
+      <param name="loadData" value="true"/>
+      <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[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_TICCalculator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help>
   <expand macro="references"/>
 </tool>