Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/3.1+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.8+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.3.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.1.0 |
FeatureFinderMetabo |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 3.1 | package |
openms-thirdparty | 3.1 | package |
blast | 2.14.1 | package |
ctdopts | 1.5 | 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': '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 && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_chrom && #end if ## Main program call set -o pipefail && FeatureFinderMetabo -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'FeatureFinderMetabo.ctd' '$args_json' '$hardcoded_json' && FeatureFinderMetabo -ini FeatureFinderMetabo.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${gxy2omsext("featurexml")}' #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_chrom 'out_chrom/output.${gxy2omsext("mzml")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("featurexml")}' '$out' #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_chrom/output.${gxy2omsext("mzml")}' '$out_chrom' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'FeatureFinderMetabo.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: FeatureFinderMetabo_1_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 20.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: 300.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: metabolites (5% RMS) algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: False algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FeatureFinderMetabo_1_input.mzML value |
Test-2 |
in: FeatureFinderMetabo_2_input.mzML algorithm|common|noise_threshold_int: 100.0 algorithm|common|chrom_peak_snr: 0.0 algorithm|common|chrom_fwhm: 100.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: median algorithm|mtd|trace_termination_criterion: sample_rate algorithm|mtd|trace_termination_outliers: 2 algorithm|mtd|min_sample_rate: 0.01 algorithm|mtd|min_trace_length: 30.0 algorithm|mtd|max_trace_length: 3000.0 algorithm|epd|enabled: False algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 10.0 algorithm|epd|max_fwhm: 80.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 4.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: False algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: False algorithm|ffm|use_smoothed_intensities: False algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FeatureFinderMetabo_2_input.mzML value |
Test-3 |
in: FeatureFinderMetabo_3_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: -1.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: fixed algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_chrom_FLAG'] |
name: value name: value name: value |
FeatureFinderMetabo_3_input.mzML value |
Test-4 |
in: FeatureFinderMetabo_3_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: -1.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: fixed algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: True algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_chrom_FLAG'] |
name: value name: value name: value |
FeatureFinderMetabo_3_input.mzML value |
Test-5 |
in: FeatureFinderMetabo_1_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 20.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: max_height algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: 300.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: metabolites (5% RMS) algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: False algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FeatureFinderMetabo_1_input.mzML value |