Repository revision
7:0fc9ae55bcfc

Repository 'openms_percolatoradapter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter

PercolatorAdapter tool metadata
Miscellaneous
Facilitate input to Percolator and reintegrate.
PercolatorAdapter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.6+galaxy0
2.6+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.6+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.3.0
PercolatorAdapter
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.6 package
openms-thirdparty 2.6 package
blast 2.9.0 package
ctdopts 1.4 package
Additional information about this tool
#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', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', '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', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', '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
#if $in:
  mkdir in &&
  ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
#end if
#if $in_decoy:
  mkdir in_decoy &&
  ${ ' '.join(["ln -s '%s' 'in_decoy/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _]) }
#end if
#if $in_osw:
  mkdir in_osw &&
  ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
#end if
mkdir out &&
#if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_pin &&
#end if
#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_pout_target &&
#end if
#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_pout_decoy &&
#end if
#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_pout_target_proteins &&
#end if
#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_pout_decoy_proteins &&
#end if
#if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir weights &&
#end if
#if $adv_opts_cond.adv_opts_selector=='advanced':
  #if $adv_opts_cond.init_weights:
    mkdir adv_opts_cond.init_weights &&
    ln -s '$adv_opts_cond.init_weights' 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)' &&
  #end if
  #if $adv_opts_cond.fasta:
    mkdir adv_opts_cond.fasta &&
    ln -s '$adv_opts_cond.fasta' 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' &&
  #end if
#end if

## Main program call

set -o pipefail &&
PercolatorAdapter -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' 'PercolatorAdapter.ctd' '$args_json' '$hardcoded_json' &&
PercolatorAdapter -ini PercolatorAdapter.ctd
#if $in:
  -in
  ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
#end if
#if $in_decoy:
  -in_decoy
  ${' '.join(["'in_decoy/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])}
#end if
#if $in_osw:
  -in_osw
  'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)'
#end if
-out
'out/output.${out_type}'
#if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_pin
  'out_pin/output.${gxy2omsext("tabular")}'
#end if
#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_pout_target
  'out_pout_target/output.${gxy2omsext("tabular")}'
#end if
#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_pout_decoy
  'out_pout_decoy/output.${gxy2omsext("tabular")}'
#end if
#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_pout_target_proteins
  'out_pout_target_proteins/output.${gxy2omsext("tabular")}'
#end if
#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_pout_decoy_proteins
  'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}'
#end if
#if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -weights
  'weights/output.${gxy2omsext("tabular")}'
#end if
#if $adv_opts_cond.adv_opts_selector=='advanced':
  #if $adv_opts_cond.init_weights:
    -init_weights
    'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)'
  #end if
  #if $adv_opts_cond.fasta:
    -fasta
    'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)'
  #end if
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${out_type}' '$out'
#if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin'
#end if
#if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_pout_target/output.${gxy2omsext("tabular")}' '$out_pout_target'
#end if
#if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_pout_decoy/output.${gxy2omsext("tabular")}' '$out_pout_decoy'
#end if
#if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_pout_target_proteins/output.${gxy2omsext("tabular")}' '$out_pout_target_proteins'
#end if
#if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}' '$out_pout_decoy_proteins'
#end if
#if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'weights/output.${gxy2omsext("tabular")}' '$weights'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv 'PercolatorAdapter.ctd' '$ctd_out'
#end if
None
False
False
Functional tests
name inputs outputs required files
Test-1 in: PercolatorAdapter_1.idXML
out_type: idXML
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms2
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.5
adv_opts_cond|trainFDR: 0.5
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
PercolatorAdapter_1.idXML
value
Test-2 in_osw: PercolatorAdapter_2.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms1
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
PercolatorAdapter_2.osw
value
Test-3 in_osw: PercolatorAdapter_2_out1.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms2
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
PercolatorAdapter_2_out1.osw
value
Test-4 in_osw: PercolatorAdapter_3_out1.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: transition
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
PercolatorAdapter_3_out1.osw
value
Test-5 in: PercolatorAdapter_1.idXML
out_type: idXML
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms2
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.5
adv_opts_cond|trainFDR: 0.5
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_pin_FLAG']
name: value
name: value
name: value
PercolatorAdapter_1.idXML
value