<!--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: [Identification of Proteins/Peptides (SearchEngines)]-->
<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
  <macros>
    <token name="@EXECUTABLE@">NovorAdapter</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 $novorFile:
  mkdir novorFile &&
  cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.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($in.ext)'
-out
'out/output.${gxy2omsext("idxml")}'
#if $novorFile:
  -novorFile
  'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("idxml")}' '$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[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
    <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
      <option value="Trypsin" selected="true">Trypsin</option>
      <expand macro="list_string_san" name="enzyme"/>
    </param>
    <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
      <option value="CID" selected="true">CID</option>
      <option value="HCD">HCD</option>
      <expand macro="list_string_san" name="fragmentation"/>
    </param>
    <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
      <option value="Trap" selected="true">Trap</option>
      <option value="TOF">TOF</option>
      <option value="FT">FT</option>
      <expand macro="list_string_san" name="massAnalyzer"/>
    </param>
    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
    <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
    <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
      <expand macro="list_string_san" name="precursor_error_units"/>
    </param>
    <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>
      <option value="Biotin (N-term)">Biotin (N-term)</option>
      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
      <option value="Carbamyl (K)">Carbamyl (K)</option>
      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
      <option value="Deamidated (NQ)">Deamidated (NQ)</option>
      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
      <option value="Dioxidation (M)">Dioxidation (M)</option>
      <option value="Methyl (C-term)">Methyl (C-term)</option>
      <option value="Methyl (DE)">Methyl (DE)</option>
      <option value="Oxidation (M)">Oxidation (M)</option>
      <option value="Oxidation (HW)">Oxidation (HW)</option>
      <option value="Phospho (ST)">Phospho (ST)</option>
      <option value="Phospho (Y)">Phospho (Y)</option>
      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
      <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
      <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
      <option value="Sodium (C-term)">Sodium (C-term)</option>
      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="variable_modifications"/>
    </param>
    <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
      <option value="Acetyl (K)">Acetyl (K)</option>
      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
      <option value="Amidated (C-term)">Amidated (C-term)</option>
      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
      <option value="Biotin (K)">Biotin (K)</option>
      <option value="Biotin (N-term)">Biotin (N-term)</option>
      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
      <option value="Carbamyl (K)">Carbamyl (K)</option>
      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
      <option value="Deamidated (NQ)">Deamidated (NQ)</option>
      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
      <option value="Dioxidation (M)">Dioxidation (M)</option>
      <option value="Methyl (C-term)">Methyl (C-term)</option>
      <option value="Methyl (DE)">Methyl (DE)</option>
      <option value="Oxidation (M)">Oxidation (M)</option>
      <option value="Oxidation (HW)">Oxidation (HW)</option>
      <option value="Phospho (ST)">Phospho (ST)</option>
      <option value="Phospho (Y)">Phospho (Y)</option>
      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
      <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
      <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
      <option value="Sodium (C-term)">Sodium (C-term)</option>
      <option value="Sodium (DE)">Sodium (DE)</option>
      <option value="Sulfo (STY)">Sulfo (STY)</option>
      <option value="Trimethyl (RK)">Trimethyl (RK)</option>
      <expand macro="list_string_san" name="fixed_modifications"/>
    </param>
    <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
      <option value="I">I</option>
      <option value="U">U</option>
      <expand macro="list_string_san" name="forbiddenResidues"/>
    </param>
    <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
    <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 ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_NovorAdapter_1 -->
  </tests>
  <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.


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