<?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: [Targeted Experiments]-->
<tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
  <macros>
    <token name="@EXECUTABLE@">MRMMapper</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir tr &&
ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-tr
'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
-out
'out/output.${gxy2omsext("mzml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mzml")}' '$out'
#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 name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
    <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
      <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
      <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/>
      <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_MRMMapper"/>
    <expand macro="manutest_MRMMapper"/>
  </tests>
  <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)


For more information, visit http://www.openms.de/documentation/TOPP_MRMMapper.html]]></help>
  <expand macro="references"/>
</tool>