Repository revision
9:d02fe0dfd2dc

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

MapAlignerPoseClustering tool metadata
Miscellaneous
Corrects retention time distortions between maps using a pose clustering approach.
MapAlignerPoseClustering
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapalignerposeclustering/MapAlignerPoseClustering/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_mapalignerposeclustering/MapAlignerPoseClustering/2.8+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapalignerposeclustering/MapAlignerPoseClustering/2.6+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapalignerposeclustering/MapAlignerPoseClustering/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapalignerposeclustering/MapAlignerPoseClustering/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapalignerposeclustering/MapAlignerPoseClustering/2.2.0
MapAlignerPoseClustering
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
Functional tests
name inputs outputs required files
Test-1 in: ['MapAlignerPoseClustering_1_input1.featureXML', 'MapAlignerPoseClustering_1_input2.featureXML', 'MapAlignerPoseClustering_1_input3.featureXML']
reference|index: 0
algorithm|max_num_peaks_considered: 400
algorithm|superimposer|mz_pair_max_distance: 0.5
algorithm|superimposer|rt_pair_distance_fraction: 0.1
algorithm|superimposer|num_used_points: 2000
algorithm|superimposer|scaling_bucket_size: 0.005
algorithm|superimposer|shift_bucket_size: 3.0
algorithm|superimposer|max_shift: 1000.0
algorithm|superimposer|max_scaling: 2.0
algorithm|superimposer|dump_buckets:
algorithm|superimposer|dump_pairs:
algorithm|pairfinder|second_nearest_gap: 2.0
algorithm|pairfinder|use_identifications: False
algorithm|pairfinder|ignore_charge: True
algorithm|pairfinder|ignore_adduct: True
algorithm|pairfinder|distance_RT|max_difference: 30.0
algorithm|pairfinder|distance_RT|exponent: 1.0
algorithm|pairfinder|distance_RT|weight: 1.0
algorithm|pairfinder|distance_MZ|max_difference: 0.3
algorithm|pairfinder|distance_MZ|unit: Da
algorithm|pairfinder|distance_MZ|exponent: 2.0
algorithm|pairfinder|distance_MZ|weight: 1.0
algorithm|pairfinder|distance_intensity|exponent: 1.0
algorithm|pairfinder|distance_intensity|weight: 0.0
algorithm|pairfinder|distance_intensity|log_transform: disabled
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG', 'trafo_out_FLAG']
name: value
MapAlignerPoseClustering_1_input1.featureXML
MapAlignerPoseClustering_1_input2.featureXML
MapAlignerPoseClustering_1_input3.featureXML
value
Test-2 in: ['MapAlignerPoseClustering_2_input1.mzML', 'MapAlignerPoseClustering_2_input2.mzML', 'MapAlignerPoseClustering_2_input3.mzML']
reference|index: 0
algorithm|max_num_peaks_considered: 400
algorithm|superimposer|mz_pair_max_distance: 0.5
algorithm|superimposer|rt_pair_distance_fraction: 0.1
algorithm|superimposer|num_used_points: 2000
algorithm|superimposer|scaling_bucket_size: 0.005
algorithm|superimposer|shift_bucket_size: 3.0
algorithm|superimposer|max_shift: 1000.0
algorithm|superimposer|max_scaling: 2.0
algorithm|superimposer|dump_buckets:
algorithm|superimposer|dump_pairs:
algorithm|pairfinder|second_nearest_gap: 2.0
algorithm|pairfinder|use_identifications: False
algorithm|pairfinder|ignore_charge: False
algorithm|pairfinder|ignore_adduct: True
algorithm|pairfinder|distance_RT|max_difference: 100.0
algorithm|pairfinder|distance_RT|exponent: 1.0
algorithm|pairfinder|distance_RT|weight: 1.0
algorithm|pairfinder|distance_MZ|max_difference: 0.3
algorithm|pairfinder|distance_MZ|unit: Da
algorithm|pairfinder|distance_MZ|exponent: 2.0
algorithm|pairfinder|distance_MZ|weight: 1.0
algorithm|pairfinder|distance_intensity|exponent: 1.0
algorithm|pairfinder|distance_intensity|weight: 0.0
algorithm|pairfinder|distance_intensity|log_transform: disabled
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG']
name: value
MapAlignerPoseClustering_2_input1.mzML
MapAlignerPoseClustering_2_input2.mzML
MapAlignerPoseClustering_2_input3.mzML
value
Test-3 in: ['MapAlignerPoseClustering_1_input2.featureXML', 'MapAlignerPoseClustering_1_input3.featureXML']
reference|file: MapAlignerPoseClustering_1_input1.featureXML
reference|index: 0
algorithm|max_num_peaks_considered: 400
algorithm|superimposer|mz_pair_max_distance: 0.5
algorithm|superimposer|rt_pair_distance_fraction: 0.1
algorithm|superimposer|num_used_points: 2000
algorithm|superimposer|scaling_bucket_size: 0.005
algorithm|superimposer|shift_bucket_size: 3.0
algorithm|superimposer|max_shift: 1000.0
algorithm|superimposer|max_scaling: 2.0
algorithm|superimposer|dump_buckets:
algorithm|superimposer|dump_pairs:
algorithm|pairfinder|second_nearest_gap: 2.0
algorithm|pairfinder|use_identifications: False
algorithm|pairfinder|ignore_charge: True
algorithm|pairfinder|ignore_adduct: True
algorithm|pairfinder|distance_RT|max_difference: 30.0
algorithm|pairfinder|distance_RT|exponent: 1.0
algorithm|pairfinder|distance_RT|weight: 1.0
algorithm|pairfinder|distance_MZ|max_difference: 0.3
algorithm|pairfinder|distance_MZ|unit: Da
algorithm|pairfinder|distance_MZ|exponent: 2.0
algorithm|pairfinder|distance_MZ|weight: 1.0
algorithm|pairfinder|distance_intensity|exponent: 1.0
algorithm|pairfinder|distance_intensity|weight: 0.0
algorithm|pairfinder|distance_intensity|log_transform: disabled
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG']
name: value
MapAlignerPoseClustering_1_input2.featureXML
MapAlignerPoseClustering_1_input3.featureXML
MapAlignerPoseClustering_1_input1.featureXML
value
Test-4 in: ['MapAlignerPoseClustering_1_input1.featureXML', 'MapAlignerPoseClustering_1_input2.featureXML']
reference|index: 2
algorithm|max_num_peaks_considered: 400
algorithm|superimposer|mz_pair_max_distance: 0.5
algorithm|superimposer|rt_pair_distance_fraction: 0.1
algorithm|superimposer|num_used_points: 2000
algorithm|superimposer|scaling_bucket_size: 0.005
algorithm|superimposer|shift_bucket_size: 3.0
algorithm|superimposer|max_shift: 1000.0
algorithm|superimposer|max_scaling: 2.0
algorithm|superimposer|dump_buckets:
algorithm|superimposer|dump_pairs:
algorithm|pairfinder|second_nearest_gap: 2.0
algorithm|pairfinder|use_identifications: False
algorithm|pairfinder|ignore_charge: True
algorithm|pairfinder|ignore_adduct: True
algorithm|pairfinder|distance_RT|max_difference: 30.0
algorithm|pairfinder|distance_RT|exponent: 1.0
algorithm|pairfinder|distance_RT|weight: 1.0
algorithm|pairfinder|distance_MZ|max_difference: 0.3
algorithm|pairfinder|distance_MZ|unit: Da
algorithm|pairfinder|distance_MZ|exponent: 2.0
algorithm|pairfinder|distance_MZ|weight: 1.0
algorithm|pairfinder|distance_intensity|exponent: 1.0
algorithm|pairfinder|distance_intensity|weight: 0.0
algorithm|pairfinder|distance_intensity|log_transform: disabled
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'trafo_out_FLAG']
name: value
MapAlignerPoseClustering_1_input1.featureXML
MapAlignerPoseClustering_1_input2.featureXML
value