<!--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="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Generates decoys according to different models for a specific TraML</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</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 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($in.ext)'
-out
'out/output.${out_type}'

## Postprocessing
&& mv 'out/output.${out_type}' '$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="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
      <option value="TraML">traml</option>
      <option value="pqp">pqp</option>
      <option value="tsv">tabular (tsv)</option>
      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
      <expand macro="list_string_san" name="out_type"/>
    </param>
    <param argument="-method" type="select" label="Decoy generation method" help="">
      <option value="shuffle" selected="true">shuffle</option>
      <option value="pseudo-reverse">pseudo-reverse</option>
      <option value="reverse">reverse</option>
      <option value="shift">shift</option>
      <expand macro="list_string_san" name="method"/>
    </param>
    <param argument="-decoy_tag" type="text" value="DECOY_" label="decoy tag" help="">
      <expand macro="list_string_san" name="decoy_tag"/>
    </param>
    <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/>
    <expand macro="adv_opts_macro">
      <param argument="-min_decoy_fraction" type="float" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
      <param argument="-aim_decoy_fraction" type="float" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/>
      <param argument="-shuffle_max_attempts" type="integer" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
      <param argument="-shuffle_sequence_identity_threshold" type="float" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
      <param argument="-shift_precursor_mz_shift" type="float" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
      <param argument="-shift_product_mz_shift" type="float" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
      <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
      <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help="">
        <expand macro="list_string_san" name="allowed_fragment_types"/>
      </param>
      <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help="">
        <expand macro="list_string_san" name="allowed_fragment_charges"/>
      </param>
      <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
      <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
      <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" 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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="traml">
      <change_format>
        <when input="out_type" value="pqp" format="pqp"/>
        <when input="out_type" value="tsv" format="tabular"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_OpenSwathDecoyGenerator_test_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="min_decoy_fraction" value="0.8"/>
        <param name="aim_decoy_fraction" value="1.0"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="shift_precursor_mz_shift" value="0.0"/>
        <param name="shift_product_mz_shift" value="20.0"/>
        <param name="product_mz_threshold" value="0.025"/>
        <param name="allowed_fragment_types" value="b,y"/>
        <param name="allowed_fragment_charges" value="1,2,3,4"/>
        <param name="enable_detection_specific_losses" value="false"/>
        <param name="enable_detection_unspecific_losses" value="false"/>
        <param name="separate" value="true"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
      <output name="out" value="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="method" value="pseudo-reverse"/>
      <param name="decoy_tag" value="DECOY_"/>
      <param name="switchKR" value="false"/>
      <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>
    <!-- TOPP_OpenSwathDecoyGenerator_test_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="min_decoy_fraction" value="0.8"/>
        <param name="aim_decoy_fraction" value="1.0"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="shift_precursor_mz_shift" value="0.0"/>
        <param name="shift_product_mz_shift" value="20.0"/>
        <param name="product_mz_threshold" value="0.8"/>
        <param name="allowed_fragment_types" value="b,y"/>
        <param name="allowed_fragment_charges" value="1,2,3,4"/>
        <param name="enable_detection_specific_losses" value="false"/>
        <param name="enable_detection_unspecific_losses" value="false"/>
        <param name="separate" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
      <output name="out" value="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="method" value="pseudo-reverse"/>
      <param name="decoy_tag" value="DECOY_"/>
      <param name="switchKR" value="false"/>
      <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>
    <!-- TOPP_OpenSwathDecoyGenerator_test_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="min_decoy_fraction" value="0.8"/>
        <param name="aim_decoy_fraction" value="1.0"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="shift_precursor_mz_shift" value="0.0"/>
        <param name="shift_product_mz_shift" value="20.0"/>
        <param name="product_mz_threshold" value="0.025"/>
        <param name="allowed_fragment_types" value="b,y"/>
        <param name="allowed_fragment_charges" value="1,2,3,4"/>
        <param name="enable_detection_specific_losses" value="false"/>
        <param name="enable_detection_unspecific_losses" value="false"/>
        <param name="separate" value="true"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
      <output name="out" value="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="method" value="pseudo-reverse"/>
      <param name="decoy_tag" value="DECOY_"/>
      <param name="switchKR" value="false"/>
      <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>
    <!-- TOPP_OpenSwathDecoyGenerator_test_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="min_decoy_fraction" value="0.4"/>
        <param name="aim_decoy_fraction" value="1.0"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="shift_precursor_mz_shift" value="0.0"/>
        <param name="shift_product_mz_shift" value="20.0"/>
        <param name="product_mz_threshold" value="0.025"/>
        <param name="allowed_fragment_types" value="b,y"/>
        <param name="allowed_fragment_charges" value="1,2,3,4"/>
        <param name="enable_detection_specific_losses" value="true"/>
        <param name="enable_detection_unspecific_losses" value="true"/>
        <param name="separate" value="true"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
      <output name="out" value="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="method" value="pseudo-reverse"/>
      <param name="decoy_tag" value="DECOY_"/>
      <param name="switchKR" value="true"/>
      <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>
    <!-- TOPP_OpenSwathDecoyGenerator_test_5 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="min_decoy_fraction" value="0.4"/>
        <param name="aim_decoy_fraction" value="1.0"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="shift_precursor_mz_shift" value="0.0"/>
        <param name="shift_product_mz_shift" value="20.0"/>
        <param name="product_mz_threshold" value="0.025"/>
        <param name="allowed_fragment_types" value="b,y"/>
        <param name="allowed_fragment_charges" value="1,2,3,4"/>
        <param name="enable_detection_specific_losses" value="false"/>
        <param name="enable_detection_unspecific_losses" value="false"/>
        <param name="separate" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathDecoyGenerator_input_5.tsv" ftype="tabular"/>
      <output name="out" value="OpenSwathDecoyGenerator_output_5.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="method" value="pseudo-reverse"/>
      <param name="decoy_tag" value="DECOY_"/>
      <param name="switchKR" value="false"/>
      <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[Generates decoys according to different models for a specific TraML


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