| Previous changeset 1:20429f4c1b95 (2020-01-22) Next changeset 3:ace92c9a4653 (2021-01-27) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit afbe0da7a518d6fc60ea066917b1e567c8c42391" |
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modified:
graphprot_predict_wrapper.py graphprot_train_predict.xml |
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| diff -r 20429f4c1b95 -r 7bbb7bf6304f graphprot_predict_wrapper.py --- a/graphprot_predict_wrapper.py Wed Jan 22 10:14:41 2020 -0500 +++ b/graphprot_predict_wrapper.py Mon Jan 27 18:37:05 2020 -0500 |
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| @@ -186,11 +186,11 @@ # Read in FASTA sequences to check for uppercase sequences. seqs_dic = gplib.read_fasta_into_dic(args.in_fa) c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic) - assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept))" + assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept)" if not args.ws_pred: # Check for lowercase sequences. c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic) - assert not c_lc_nt, "lowercase nucleotides not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept))" + assert not c_lc_nt, "lowercase nucleotides in input .fa not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept)" # Check .bed. if args.genomic_sites_bed: # An array of checks, marvelous. |
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| diff -r 20429f4c1b95 -r 7bbb7bf6304f graphprot_train_predict.xml --- a/graphprot_train_predict.xml Wed Jan 22 10:14:41 2020 -0500 +++ b/graphprot_train_predict.xml Mon Jan 27 18:37:05 2020 -0500 |
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| @@ -154,7 +154,7 @@ </data> <data name="str_motif_out_file" format="txt" from_work_dir="GraphProt.structure_motif" label="${tool.name} on ${on_string}: GraphProt structure motif text file"> - <filter>action_type["action_type_selector"] == "train" and not action_type["training_options"]["disable_motifs"]</filter> + <filter>action_type["action_type_selector"] == "train" and not action_type["training_options"]["disable_motifs"] and action_type["train_str_model"]</filter> </data> <data name="str_motif_png_out_file" format="png" from_work_dir="GraphProt.structure_motif.png" label="${tool.name} on ${on_string}: GraphProt structure motif png file"> @@ -193,7 +193,7 @@ <tests> - <test expect_num_outputs="5"> + <test expect_num_outputs="4"> <param name="action_type_selector" value="train"/> <param name="pos_fasta_file" value="test_positives.train.fa" ftype="fasta"/> <param name="neg_fasta_file" value="test_negatives.train.fa" ftype="fasta"/> |