<!--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 and OpenSWATH]-->
<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>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir pair_in &&
cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
mkdir out &&
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir feature_out &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-pair_in
'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)'
-out
'out/output.${gxy2omsext("consensusxml")}'
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -feature_out
  'feature_out/output.${gxy2omsext("featurexml")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'feature_out/output.${gxy2omsext("featurexml")}' '$feature_out'
#end if
#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="-in" type="data" format="featurexml" 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" 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 argument="-mass_tolerance" type="float" 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" 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" 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" 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="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
    <data name="feature_out" label="${tool.name} on ${on_string}: feature_out" format="featurexml">
      <filter>OPTIONAL_OUTPUTS is not None and "feature_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- 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 https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMPairFinder.html]]></help>
  <expand macro="references"/>
</tool>