Repository revision
8:aa62f8f48dd4

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

TargetedFileConverter tool metadata
Miscellaneous
Converts different transition files for targeted proteomics / metabolomics analysis.
TargetedFileConverter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0
2.5+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.2.0
TargetedFileConverter
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.5 package
openms-thirdparty 2.5 package
blast 2.9.0 package
openjdk 8.0.192 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: ConvertTSVToTraML_1_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_1_input.tsv
value
Test-2 in: ConvertTSVToTraML_2_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: minutes
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_2_input.tsv
value
Test-3 in: ConvertTSVToTraML_2_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: seconds
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_2_input.tsv
value
Test-4 in: ConvertTSVToTraML_4_input.mrm
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_4_input.mrm
value
Test-5 in: ConvertTSVToTraML_5_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_5_input.tsv
value
Test-6 in: ConvertTSVToTraML_6_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_6_input.tsv
value
Test-7 in: ConvertTSVToTraML_7_input_Skyline.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_7_input_Skyline.tsv
value
Test-8 in: TargetedFileConverter_1_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_1_output.pqp.tmp
value
Test-9 in: TargetedFileConverter_1_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: True
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
TargetedFileConverter_1_output.pqp.tmp
value
Test-10 in: TargetedFileConverter_3_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_3_output.pqp.tmp
value
Test-11 in: TargetedFileConverter_3_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: True
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
TargetedFileConverter_3_output.pqp.tmp
value
Test-12 in: TargetedFileConverter_10_output.TraML.tmp
out_type: tsv
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_10_output.TraML.tmp
value
Test-13 in: TargetedFileConverter_11_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_11_output.pqp.tmp
value
Test-14 in: TargetedFileConverter_8_output.TraML.tmp
out_type: tsv
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: True
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_8_output.TraML.tmp
value
Test-15 in: TargetedFileConverter_9_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: True
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_9_output.pqp.tmp
value
Test-16 in: ConvertTSVToTraML_output.TraML
out_type: tsv
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_output.TraML
value
Test-17 in: TargetedFileConverter_12_output.pqp.tmp
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: True
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_12_output.pqp.tmp
value
Test-18 in: TargetedFileConverter_12_input.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
TargetedFileConverter_12_input.tsv
value
Test-19 in: ConvertTSVToTraML_5_output.TraML
out_type: tsv
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
ConvertTSVToTraML_5_output.TraML
value
Test-20 in: AssayGeneratorMetabo_ams_uku_output_consensus.tsv
out_type: TraML
algorithm|retentionTimeInterpretation: iRT
algorithm|override_group_label_check: False
algorithm|force_invalid_mods: False
adv_opts_cond|legacy_traml_id: False
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
AssayGeneratorMetabo_ams_uku_output_consensus.tsv
value