diff DTAExtractor.xml @ 17:79706b7647c3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:17:40 +0000
parents d8b1ec05fbd7
children 78024781d209
line wrap: on
line diff
--- a/DTAExtractor.xml	Fri Nov 06 20:06:46 2020 +0000
+++ b/DTAExtractor.xml	Thu Dec 01 19:17:40 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: [File Handling]-->
-<tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Extracts spectra of an MS run file to several files in DTA format.</description>
   <macros>
     <token name="@EXECUTABLE@">DTAExtractor</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -38,23 +36,23 @@
     <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 name="out" argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
+      <expand macro="list_string_san" name="out"/>
     </param>
-    <param name="mz" argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
-      <expand macro="list_string_san"/>
+    <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
+      <expand macro="list_string_san" name="mz"/>
     </param>
-    <param name="rt" argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
+      <expand macro="list_string_san" name="rt"/>
     </param>
-    <param name="level" argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
+      <expand macro="list_string_san" name="level"/>
     </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">
@@ -69,13 +67,64 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_DTAExtractor"/>
-    <expand macro="manutest_DTAExtractor"/>
+  <tests><!-- TOPP_DTAExtractor_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="DTAExtractor_1_input.mzML"/>
+      <param name="out" value="DTAExtractor"/>
+      <param name="mz" value=":"/>
+      <param name="rt" value=":61"/>
+      <param name="level" value="1,2,3"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_DTAExtractor_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="DTAExtractor_1_input.mzML"/>
+      <param name="out" value="DTAExtractor"/>
+      <param name="mz" value=":"/>
+      <param name="rt" value=":"/>
+      <param name="level" value="1"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_DTAExtractor_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="DTAExtractor_1_input.mzML"/>
+      <param name="out" value="DTAExtractor"/>
+      <param name="mz" value=":1000"/>
+      <param name="rt" value=":"/>
+      <param name="level" value="2"/>
+      <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[Extracts spectra of an MS run file to several files in DTA format.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_DTAExtractor.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help>
   <expand macro="references"/>
 </tool>