diff MRMPairFinder.xml @ 12:bd57c94d50fb draft

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

--- a/MRMPairFinder.xml	Fri Nov 06 19:43:32 2020 +0000
+++ b/MRMPairFinder.xml	Thu Dec 01 19:00:25 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="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
   <macros>
     <token name="@EXECUTABLE@">MRMPairFinder</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -58,15 +56,15 @@
     <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 featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
-    <param name="pair_in" argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
+    <param argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <param name="mass_tolerance" argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
-      <param name="RT_tolerance" argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
-      <param name="RT_pair_tolerance" argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
-      <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="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
+      <param argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
+      <param argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
+      <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">
@@ -83,13 +81,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MRMPairFinder"/>
-    <expand macro="manutest_MRMPairFinder"/>
-  </tests>
+  <tests><!-- TODO no idea about a useful input for pair_in -->
+</tests>
   <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MRMPairFinder.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMPairFinder.html]]></help>
   <expand macro="references"/>
 </tool>