#def quote(s):
    #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
    #set $q = False
    #for $i, $p in enumerate($s):
        #if $p == "":
            #continue
        #end if
        #if $p.startswith('"'):
            #set $q = True
        #end if
##        #if p.startswith('-'):
##            #set p = "\\" + p
##        #elif p.startswith('"-'):
##            #set p = "\\" + p[1:]
##        #end if
        #if not $q:
            #set $s[i] = '"%s"' % p
        #end if
        #if $p.endswith('"'):
            #set $q = False
        #end if
    #end for
    #return " ".join($s)
#end def
  
#def oms2gxyext(o)
    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
    #return m[o]
#end def
#def gxy2omsext(g)
    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
    #return m[g]
#end def

#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir tr &&
ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
#if $tr_irt:
  mkdir tr_irt &&
  ln -s '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' &&
#end if
#if $tr_irt_nonlinear:
  mkdir tr_irt_nonlinear &&
  ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
#end if
#if $swath_windows_file:
  mkdir swath_windows_file &&
  ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
#end if
#if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_features &&
#end if
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_tsv &&
#end if
#if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_osw &&
#end if
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_chrom &&
#end if
#if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_qc &&
#end if
#if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir Debugging_irt_mzml &&
#end if
#if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir Debugging_irt_trafo &&
#end if
  #if $adv_opts.rt_norm:
    mkdir adv_opts.rt_norm &&
    ln -s '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' &&
  #end if

## Main program call

set -o pipefail &&
OpenSwathWorkflow -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' 'OpenSwathWorkflow.ctd' '$args_json' '$hardcoded_json' &&
OpenSwathWorkflow -ini OpenSwathWorkflow.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-tr
'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
#if $tr_irt:
  -tr_irt
  'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)'
#end if
#if $tr_irt_nonlinear:
  -tr_irt_nonlinear
  'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
#end if
#if $swath_windows_file:
  -swath_windows_file
  'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
#end if
#if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_features
  'out_features/output.${gxy2omsext("featurexml")}'
#end if
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_tsv
  'out_tsv/output.${gxy2omsext("tabular")}'
#end if
#if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_osw
  'out_osw/output.${gxy2omsext("osw")}'
#end if
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_chrom
  'out_chrom/output.${adv_opts.out_chrom_type}'
#end if
#if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_qc
  'out_qc/output.${gxy2omsext("json")}'
#end if
#if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -Debugging:irt_mzml
  'Debugging_irt_mzml/output.${gxy2omsext("mzml")}'
#end if
#if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -Debugging:irt_trafo
  'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}'
#end if
  #if $adv_opts.rt_norm:
    -rt_norm
    'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)'
  #end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_features/output.${gxy2omsext("featurexml")}' '$out_features'
#end if
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_tsv/output.${gxy2omsext("tabular")}' '$out_tsv'
#end if
#if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_osw/output.${gxy2omsext("osw")}' '$out_osw'
#end if
#if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_chrom/output.${adv_opts.out_chrom_type}' '$out_chrom'
#end if
#if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_qc/output.${gxy2omsext("json")}' '$out_qc'
#end if
#if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}' '$Debugging_irt_mzml'
#end if
#if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}' '$Debugging_irt_trafo'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv 'OpenSwathWorkflow.ctd' '$ctd_out'
#end if