#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': 'xsd', 'zip': 'zip'}
    #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', 'xsd': 'xsd', 'zip': 'zip'}
    #return m[g]
#end def

#import re

## Preprocessing
mkdir in_cm &&
cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
#if $in_raw_cond.in_raw:
  mkdir in_raw_cond.in_raw &&
  #if $in_raw_cond.in_raw_select == "no"
  mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} && 
  ${' '.join(["cp '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
  #else
  cp '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
  #end if
#end if
#if $in_postFDR_cond.in_postFDR:
  mkdir in_postFDR_cond.in_postFDR &&
  #if $in_postFDR_cond.in_postFDR_select == "no"
  mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} && 
  ${' '.join(["cp '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
  #else
  cp '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
  #end if
#end if
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out &&
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_cm &&
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_feat &&
  mkdir ${' '.join(["'out_feat/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} && 
#end if
#if $in_contaminants:
  mkdir in_contaminants &&
  cp '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
#end if
#if $in_fasta:
  mkdir in_fasta &&
  cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
#end if
#if $in_trafo_cond.in_trafo:
  mkdir in_trafo_cond.in_trafo &&
  #if $in_trafo_cond.in_trafo_select == "no"
  mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} && 
  ${' '.join(["cp '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
  #else
  cp '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
  #end if
#end if

## Main program call

set -o pipefail &&
QualityControl -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' 'QualityControl.ctd' '$args_json' '$hardcoded_json' &&
QualityControl -ini QualityControl.ctd
-in_cm
'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
#if $in_raw_cond.in_raw:
  -in_raw
  #if $in_raw_cond.in_raw_select == "no"
  ${' '.join(["'in_raw_cond.in_raw/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
  #else
  'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)'
  #end if
#end if
#if $in_postFDR_cond.in_postFDR:
  -in_postFDR
  #if $in_postFDR_cond.in_postFDR_select == "no"
  ${' '.join(["'in_postFDR_cond.in_postFDR/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
  #else
  'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)'
  #end if
#end if
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out
  'out/output.${gxy2omsext("mztab")}'
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_cm
  'out_cm/output.${gxy2omsext("consensusxml")}'
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_feat
  ${' '.join(["'out_feat/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("featurexml")) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
#end if
#if $in_contaminants:
  -in_contaminants
  'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
#end if
#if $in_fasta:
  -in_fasta
  'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)'
#end if
#if $in_trafo_cond.in_trafo:
  -in_trafo
  #if $in_trafo_cond.in_trafo_select == "no"
  ${' '.join(["'in_trafo_cond.in_trafo/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
  #else
  'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)'
  #end if
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out/output.${gxy2omsext("mztab")}' '$out'
#end if
#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
#end if
#if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  ${' '.join(["&& mv -n 'out_feat/%(bn)s/%(id)s.%(gext)s' 'out_feat/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("featurexml")} for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv 'QualityControl.ctd' '$ctd_out'
#end if