<!--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="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Generates assays according to different models for a specific TraML</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAssayGenerator</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 &&
#if $swath_windows_file:
  mkdir swath_windows_file &&
  cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
#end if
#if $unimod_file:
  mkdir unimod_file &&
  cp '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.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($in.ext)'
-out
'out/output.${out_type}'
#if $swath_windows_file:
  -swath_windows_file
  'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
#end if
#if $unimod_file:
  -unimod_file
  'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)'
#end if

## 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="-min_transitions" type="integer" value="6" label="minimal number of transitions" help=""/>
    <param argument="-max_transitions" type="integer" value="6" label="maximal number of transitions" 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="-precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
    <param argument="-precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help=""/>
    <param argument="-precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
    <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
    <param argument="-product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help=""/>
    <param argument="-product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
    <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
    <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
    <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
    <expand macro="adv_opts_macro">
      <param argument="-max_num_alternative_localizations" type="integer" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
      <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
      <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
      <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
      <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
      <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_OpenSwathAssayGenerator_test_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="max_num_alternative_localizations" value="10000"/>
        <param name="disable_identification_ms2_precursors" value="false"/>
        <param name="disable_identification_specific_losses" value="false"/>
        <param name="enable_identification_unspecific_losses" value="false"/>
        <param name="enable_swath_specifity" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
      <output name="out" value="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="min_transitions" value="6"/>
      <param name="max_transitions" value="6"/>
      <param name="allowed_fragment_types" value="b,y"/>
      <param name="allowed_fragment_charges" value="2,3"/>
      <param name="enable_detection_specific_losses" value="true"/>
      <param name="enable_detection_unspecific_losses" value="false"/>
      <param name="precursor_mz_threshold" value="0.025"/>
      <param name="precursor_lower_mz_limit" value="400.0"/>
      <param name="precursor_upper_mz_limit" value="1200.0"/>
      <param name="product_mz_threshold" value="0.025"/>
      <param name="product_lower_mz_limit" value="350.0"/>
      <param name="product_upper_mz_limit" value="2000.0"/>
      <param name="enable_ipf" 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_OpenSwathAssayGenerator_test_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="max_num_alternative_localizations" value="10000"/>
        <param name="disable_identification_ms2_precursors" value="false"/>
        <param name="disable_identification_specific_losses" value="false"/>
        <param name="enable_identification_unspecific_losses" value="false"/>
        <param name="enable_swath_specifity" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
      <output name="out" value="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="min_transitions" value="6"/>
      <param name="max_transitions" value="6"/>
      <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="precursor_mz_threshold" value="0.025"/>
      <param name="precursor_lower_mz_limit" value="400.0"/>
      <param name="precursor_upper_mz_limit" value="1200.0"/>
      <param name="product_mz_threshold" value="0.025"/>
      <param name="product_lower_mz_limit" value="350.0"/>
      <param name="product_upper_mz_limit" value="2000.0"/>
      <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
      <param name="enable_ipf" 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_OpenSwathAssayGenerator_test_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="max_num_alternative_localizations" value="10000"/>
        <param name="disable_identification_ms2_precursors" value="false"/>
        <param name="disable_identification_specific_losses" value="false"/>
        <param name="enable_identification_unspecific_losses" value="false"/>
        <param name="enable_swath_specifity" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
      <output name="out" value="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
      <param name="out_type" value="TraML"/>
      <param name="min_transitions" value="6"/>
      <param name="max_transitions" value="6"/>
      <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="precursor_mz_threshold" value="0.025"/>
      <param name="precursor_lower_mz_limit" value="400.0"/>
      <param name="precursor_upper_mz_limit" value="1200.0"/>
      <param name="product_mz_threshold" value="0.025"/>
      <param name="product_lower_mz_limit" value="350.0"/>
      <param name="product_upper_mz_limit" value="2000.0"/>
      <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
      <param name="enable_ipf" 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>
  </tests>
  <help><![CDATA[Generates assays according to different models for a specific TraML


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