Repository revision
13:cab9b21eabf9

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

LuciphorAdapter tool metadata
Miscellaneous
Modification site localisation using LuciPHOr2.
LuciphorAdapter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.6+galaxy1
2.6+galaxy1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.6+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_luciphoradapter/LuciphorAdapter/2.1.0
LuciphorAdapter
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
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir id &&
ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
LuciphorAdapter -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' 'LuciphorAdapter.ctd' '$args_json' '$hardcoded_json' &&
LuciphorAdapter -ini LuciphorAdapter.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-id
'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
-out
'out/output.${gxy2omsext("idxml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv 'LuciphorAdapter.ctd' '$ctd_out'
#end if
None
False
Functional tests
name inputs outputs required files
Test-1 in: LuciphorAdapter_1_input.mzML
id: LuciphorAdapter_1_input.idXML
fragment_method: CID
fragment_mass_tolerance: 0.5
fragment_error_units: Da
min_mz: 150.0
target_modifications: ['Phospho (S)', 'Phospho (T)', 'Phospho (Y)']
neutral_losses: "sty -H3PO4 -97.97690"
decoy_mass: 79.966331
decoy_neutral_losses: "X -H3PO4 -97.97690"
max_charge_state: 5
max_peptide_length: 40
max_num_perm: 16384
modeling_score_threshold: 0.95
scoring_threshold: 0.0
min_num_psms_model: 1
run_mode: 0
rt_tolerance: 0.01
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
LuciphorAdapter_1_input.mzML
LuciphorAdapter_1_input.idXML
value