# 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 @@
-
@@ -98,7 +96,6 @@
-