Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/rnateam/graphprot_predict_profile/graphprot_predict_profile/1.1.7+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/rnateam/graphprot_predict_profile/graphprot_predict_profile/1.1.7 |
graphprot_predict_profile |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
graphprot | 1.1.7 | package |
Additional information about this tool |
#if $action_type.action_type_selector == 'train': python '$__tool_directory__/graphprot_train_wrapper.py' --data-id GraphProt --pos '$action_type.pos_fasta_file' --neg '$action_type.neg_fasta_file' $action_type.train_str_model #if $action_type.hpo_options.hpo_mode_type.hpo_mode_type_selector == 'take': --opt-set-size $action_type.hpo_options.hpo_mode_type.opt_set_size #elif $action_type.hpo_options.hpo_mode_type.hpo_mode_type_selector == 'supply': --opt-pos '$action_type.hpo_options.hpo_mode_type.pos_parop_fasta' --opt-neg '$action_type.hpo_options.hpo_mode_type.neg_parop_fasta' #end if $action_type.training_options.disable_cv $action_type.training_options.disable_motifs --min-train $action_type.training_options.min_train #elif $action_type.action_type_selector == 'predict': python '$__tool_directory__/graphprot_predict_wrapper.py' --data-id GraphProt --fasta '$action_type.input_fasta_file' --model '$action_type.model_file' --params $action_type.params_file #if $action_type.genomic_sites_bed_file: --gen-site-bed '$action_type.genomic_sites_bed_file' #end if --sc-thr $action_type.prediction_options.score_thr --max-merge-dist $action_type.prediction_options.max_merge_dist --ap-extlr $action_type.prediction_options.ap_extlr $action_type.prediction_options.conf_out $action_type.prediction_options.ws_pred_out #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
action_type|pos_fasta_file: test_positives.train.fa action_type|neg_fasta_file: test_negatives.train.fa action_type|hpo_options|hpo_mode_type|pos_parop_fasta: test_positives.parop.fa action_type|hpo_options|hpo_mode_type|neg_parop_fasta: test_negatives.parop.fa action_type|hpo_options|hpo_mode_type|hpo_mode_type_selector: supply action_type|training_options|disable_cv: True action_type|training_options|disable_motifs: False action_type|training_options|min_train: 500 action_type|action_type_selector: train |
name: value name: value name: value |
test_positives.train.fa test_negatives.train.fa test_positives.parop.fa test_negatives.parop.fa value |
Test-2 |
action_type|input_fasta_file: test_predict.fa action_type|model_file: test.model action_type|params_file: test.params action_type|genomic_sites_bed_file: test_predict.bed action_type|prediction_options|conf_out: True action_type|action_type_selector: predict |
name: value name: value name: value name: value name: value |
test_predict.fa test.model test.params test_predict.bed value |
Test-3 |
action_type|input_fasta_file: test_predict.fa action_type|model_file: test.model action_type|params_file: test.params action_type|prediction_options|ws_pred_out: True action_type|prediction_options|conf_out: True action_type|action_type_selector: predict |
name: value name: value |
test_predict.fa test.model test.params value |