diff QCEmbedder.xml @ 13:f9e709333234 draft

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

--- a/QCEmbedder.xml	Fri Nov 06 20:18:45 2020 +0000
+++ b/QCEmbedder.xml	Thu Dec 01 19:04:55 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="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Attaches a table or an image to a given qc parameter.</description>
   <macros>
     <token name="@EXECUTABLE@">QCEmbedder</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -69,23 +67,23 @@
     <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="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
-    <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
+      <expand macro="list_string_san" name="qp_att_acc"/>
     </param>
-    <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
+      <expand macro="list_string_san" name="cv_acc"/>
     </param>
-    <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
-    <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
+    <param argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="">
+      <expand macro="list_string_san" name="name"/>
     </param>
-    <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/>
-    <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
+    <param argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/>
+    <param argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
     <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">
@@ -98,13 +96,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_QCEmbedder"/>
-    <expand macro="manutest_QCEmbedder"/>
-  </tests>
+  <tests><!--TODO-->
+</tests>
   <help><![CDATA[Attaches a table or an image to a given qc parameter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCEmbedder.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCEmbedder.html]]></help>
   <expand macro="references"/>
 </tool>