<!--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>