Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.1.0 |
ProteinQuantifier |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 2.8 | package |
openms-thirdparty | 2.8 | package |
omssa | 2.1.9 | package |
blast | 2.13.0 | 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', '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)' && #if $protein_groups: mkdir protein_groups && ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && #end if #if $design: mkdir design && ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir peptide_out && #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir mztab && #end if ## Main program call set -o pipefail && ProteinQuantifier -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'ProteinQuantifier.ctd' '$args_json' '$hardcoded_json' && ProteinQuantifier -ini ProteinQuantifier.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' #if $protein_groups: -protein_groups 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' #end if #if $design: -design 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out 'out/output.${gxy2omsext("csv")}' #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -peptide_out 'peptide_out/output.${gxy2omsext("csv")}' #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -mztab 'mztab/output.${gxy2omsext("mztab")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out/output.${gxy2omsext("csv")}' '$out' #end if #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out' #end if #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'ProteinQuantifier.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: ProteinQuantifier_input.featureXML top: 3 average: median include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG'] |
name: value name: value name: value |
ProteinQuantifier_input.featureXML value |
Test-2 |
in: ProteinQuantifier_input.featureXML top: 2 average: sum include_all: True best_charge_and_fraction: True greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG'] |
name: value name: value name: value |
ProteinQuantifier_input.featureXML value |
Test-3 |
in: ProteinQuantifier_3_input.featureXML top: 2 average: mean include_all: True best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG'] |
name: value name: value name: value |
ProteinQuantifier_3_input.featureXML value |
Test-4 |
in: ProteinQuantifier_input.consensusXML top: 0 average: sum include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-5 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-6 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: True best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-7 |
in: ProteinQuantifier_input.consensusXML top: 0 average: sum include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: True format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-8 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: True format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-9 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: True best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: True format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'mztab_FLAG'] |
name: value name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-10 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: True best_charge_and_fraction: False greedy_group_resolution: False ratios: True ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: True format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-11 |
in: ProteinQuantifier_input.consensusXML top: 3 average: sum include_all: True best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: True consensus|normalize: False consensus|fix_peptides: True format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
ProteinQuantifier_input.consensusXML value |
Test-12 |
in: ProteinQuantifier_input.idXML top: 0 average: sum include_all: False best_charge_and_fraction: False greedy_group_resolution: False ratios: False ratiosSILAC: False consensus|normalize: False consensus|fix_peptides: False format|separator: format|quoting: double format|replacement: _ adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'peptide_out_FLAG'] |
name: value name: value name: value |
ProteinQuantifier_input.idXML value |