Repository revision
4:4ad83aed5c3c

Repository 'graphprot_predict_profile'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/graphprot_predict_profile

GraphProt tool metadata
Miscellaneous
GraphProt
- Train models and predict RBP binding profiles
graphprot_predict_profile
toolshed.g2.bx.psu.edu/repos/rnateam/graphprot_predict_profile/graphprot_predict_profile/1.1.7+galaxy1
1.1.7+galaxy1
None
True
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


    
None
False
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