<!--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="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Compute confidence scores for OpenSwath results</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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($in.ext)' &&
mkdir lib &&
cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
mkdir out &&
#if $trafo:
  mkdir trafo &&
  cp '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
#end if

## Main program call

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

## Postprocessing
&& mv 'out/output.${gxy2omsext("featurexml")}' '$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 argument="-in" type="data" format="featurexml" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
    <param argument="-lib" type="data" format="traml" label="Assay library" help=" select traml data sets(s)"/>
    <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
    <param argument="-decoys" type="integer" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
    <param argument="-transitions" type="integer" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
    <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
      <param name="intercept" argument="-GLM:intercept" type="float" value="3.87333466" label="Intercept term" help=""/>
      <param name="delta_rt" argument="-GLM:delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
      <param name="dist_int" argument="-GLM:dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <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="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_OpenSwathConfidenceScoring_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
      <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
      <output name="out" value="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
      <param name="decoys" value="1"/>
      <param name="transitions" value="2"/>
      <section name="GLM">
        <param name="intercept" value="3.87333466"/>
        <param name="delta_rt" value="-0.02898629"/>
        <param name="dist_int" value="-7.75880768"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Compute confidence scores for OpenSwath results


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
  <expand macro="references"/>
</tool>