# HG changeset patch # User greg # Date 1682963525 0 # Node ID 487a3c0088120e939fe8f88263abc5ef8fd9b346 # Parent c5e80637cf3df8ee99c78be82dd3d3283bc49d2a Uploaded diff -r c5e80637cf3d -r 487a3c008812 draw_amr_matrix.py --- a/draw_amr_matrix.py Tue Mar 28 13:42:30 2023 +0000 +++ b/draw_amr_matrix.py Mon May 01 17:52:05 2023 +0000 @@ -58,7 +58,7 @@ sys.exit(1) -def draw_amr_matrix(amr_feature_hits_files, amr_deletions_file, varscan_vcf_file, amr_mutation_regions_bed_file, amr_gene_drug_file, reference, reference_size, mutation_regions_dir, amr_matrix_png_dir, errors, in_test_mode): +def draw_amr_matrix(amr_feature_hits_files, amr_deletions_file, varscan_vcf_file, amr_mutation_regions_bed_file, amr_gene_drug_file, reference, reference_size, mutation_regions_dir, amr_matrix_png_dir, errors): efh = open(errors, 'w') ofh = open('process_log', 'w') @@ -192,16 +192,12 @@ ofh.write("\nAfter processing deletions, amr_to_draw: %s\n" % str(amr_to_draw)) ofh.write("\namr_to_draw.shape[0]: %s\n" % str(amr_to_draw.shape[0])) - # I have no idea why, but when running functional test with planemo + # I have no idea why, but when running functional tests with planemo # the value of amr_to_draw.shape[0] is 1 even though the tests use the # exact inputs when running outside of planeo that result in the value - # being 2. So we have to pass this in_test_mode flag in order to get - # functional tests to work. - if in_test_mode == 'true': - shape_val = 0 - else: - shape_val = 1 - if amr_to_draw.shape[0] > shape_val: + # being 2. So we cannot test with planemo unless we incorporate a hack + # like a hidden in_test_mode parameter. + if amr_to_draw.shape[0] > 1: ofh.write("\nDrawing AMR matrix...\n") present_genes = amr_to_draw['gene'].unique() present_drugs = amr_to_draw['drug'].unique() diff -r c5e80637cf3d -r 487a3c008812 draw_amr_matrix.xml --- a/draw_amr_matrix.xml Tue Mar 28 13:42:30 2023 +0000 +++ b/draw_amr_matrix.xml Mon May 01 17:52:05 2023 +0000 @@ -39,7 +39,6 @@ --reference_genome reference.fa --amr_matrix_png_dir 'amr_matrix_png_dir' --errors '$errors' ---in_test_mode '$in_test_mode' #if str($output_process_log) == 'yes': && mv 'process_log' '$process_log' #end if @@ -71,7 +70,6 @@ <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> - <param name="in_test_mode" type="hidden" value="false"/> </inputs> <outputs> <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> @@ -98,7 +96,6 @@ <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/> <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/> <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> - <param name="in_test_mode" value="true"/> <output_collection name="amr_matrix_png" type="list" count="1"> <element name="amr_matrix" ftype="png"> <assert_contents>