Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxllf/OpenPepXLLF/2.3.0 |
OpenPepXLLF |
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($in.ext)' && mkdir database && ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_idXML && #end if #if "out_mzIdentML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_mzIdentML && #end if #if "out_xquestxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_xquestxml && #end if #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_xquest_specxml && #end if #if $adv_opts.decoy_database: mkdir adv_opts.decoy_database && ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' && #end if ## Main program call set -o pipefail && OpenPepXLLF -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'OpenPepXLLF.ctd' '$args_json' '$hardcoded_json' && OpenPepXLLF -ini OpenPepXLLF.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -database 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_idXML 'out_idXML/output.${gxy2omsext("idxml")}' #end if #if "out_mzIdentML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_mzIdentML 'out_mzIdentML/output.${gxy2omsext("mzid")}' #end if #if "out_xquestxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_xquestxml 'out_xquestxml/output.${gxy2omsext("xquest.xml")}' #end if #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_xquest_specxml 'out_xquest_specxml/output.${gxy2omsext("spec.xml")}' #end if #if $adv_opts.decoy_database: -decoy_database 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_idXML/output.${gxy2omsext("idxml")}' '$out_idXML' #end if #if "out_mzIdentML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_mzIdentML/output.${gxy2omsext("mzid")}' '$out_mzIdentML' #end if #if "out_xquestxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_xquestxml/output.${gxy2omsext("xquest.xml")}' '$out_xquestxml' #end if #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_xquest_specxml/output.${gxy2omsext("spec.xml")}' '$out_xquest_specxml' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'OpenPepXLLF.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: OpenPepXLLF_input.mzML database: OpenPepXLLF_input.fasta decoy_string: decoy decoy_prefix: True precursor|mass_tolerance: 10.0 precursor|mass_tolerance_unit: ppm precursor|min_charge: 2 precursor|max_charge: 8 precursor|corrections: 4 3 2 1 0 fragment|mass_tolerance: 20.0 fragment|mass_tolerance_xlinks: 20.0 fragment|mass_tolerance_unit: ppm modifications|fixed: Carbamidomethyl (C) modifications|variable: Oxidation (M) modifications|variable_max_per_peptide: 3 peptide|min_size: 5 peptide|missed_cleavages: 3 peptide|enzyme: Trypsin cross_linker|residue1: "K" "N-term" cross_linker|residue2: "K" "N-term" cross_linker|mass: 138.0680796 cross_linker|mass_mono_link: 156.07864431 155.094628715 cross_linker|name: DSS algorithm|number_top_hits: 1 algorithm|deisotope: auto algorithm|use_sequence_tags: False algorithm|sequence_tag_min_length: 2 ions|b_ions: True ions|y_ions: True ions|a_ions: False ions|x_ions: False ions|c_ions: False ions|z_ions: False ions|neutral_losses: True adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_idXML_FLAG', 'out_mzIdentML_FLAG', 'out_xquestxml_FLAG', 'out_xquest_specxml_FLAG'] |
name: value name: value name: value name: value name: value |
OpenPepXLLF_input.mzML OpenPepXLLF_input.fasta value |
Test-2 |
in: OpenPepXLLF_input2.mzML database: OpenPepXLLF_input2.fasta decoy_string: decoy_ decoy_prefix: True precursor|mass_tolerance: 10.0 precursor|mass_tolerance_unit: ppm precursor|min_charge: 3 precursor|max_charge: 7 precursor|corrections: 1 0 fragment|mass_tolerance: 0.2 fragment|mass_tolerance_xlinks: 0.3 fragment|mass_tolerance_unit: Da modifications|fixed: Carbamidomethyl (C) modifications|variable: Oxidation (M) modifications|variable_max_per_peptide: 1 peptide|min_size: 5 peptide|missed_cleavages: 1 peptide|enzyme: Trypsin cross_linker|residue1: "D" "E" "C-term" cross_linker|residue2: "K" "S" "T" "Y" "N-term" cross_linker|mass: -18.010595 cross_linker|mass_mono_link: cross_linker|name: DMTMM algorithm|number_top_hits: 1 algorithm|deisotope: auto algorithm|use_sequence_tags: False algorithm|sequence_tag_min_length: 2 ions|b_ions: True ions|y_ions: True ions|a_ions: False ions|x_ions: False ions|c_ions: False ions|z_ions: False ions|neutral_losses: True adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_idXML_FLAG'] |
name: value name: value |
OpenPepXLLF_input2.mzML OpenPepXLLF_input2.fasta value |