--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenMSInfo.xml	Fri Jun 14 21:41:52 2024 +0000
@@ -0,0 +1,72 @@
+<!--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: [Misc / Helpers]-->
+<tool id="OpenMSInfo" name="OpenMSInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Prints configurations details of OpenMS</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenMSInfo</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+## advanced options
+  #if $adv_opts.dummy:
+    mkdir adv_opts.dummy &&
+    cp '$adv_opts.dummy' 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)' &&
+  #end if
+
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+## advanced options
+  #if $adv_opts.dummy:
+    -dummy
+    'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)'
+  #end if
+
+| tee '$stdout'
+
+## Postprocessing
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print information (flag can also be omitted)" help=""/>
+    <expand macro="adv_opts_macro">
+      <param argument="-dummy" type="data" format="txt" optional="true" label="A fake input file, which is needed for some workflow systems to call this tool" help=" select txt data sets(s)"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
+        <expand macro="list_string_san" name="test"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Prints configurations details of OpenMS.
+
+
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenMSInfo.html]]></help>
+  <expand macro="references"/>
+</tool>