comparison pima_report.xml @ 5:7177d81eb7cb draft

Uploaded
author greg
date Thu, 09 Mar 2023 17:50:28 +0000
parents 428aed51c487
children 99613333fd1f
comparison
equal deleted inserted replaced
4:428aed51c487 5:7177d81eb7cb
8 #import re 8 #import re
9 9
10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier)) 10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) 11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
12 12
13 #set blastn_version = 'unknown' 13 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
14 #for $i in $blastn_features: 14 #set blastn_version = $blastn_version.rstrip('(features)')
15 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
16 #end for
17
18 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) 15 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
19 #set dnadiff_version = $dnadiff_version.rstrip('(snps)') 16 #set dnadiff_version = $dnadiff_version.rstrip('(snps)')
20 #if str($flye_assembly_info_file) not in ['None', '']: 17 #if str($flye_assembly_info_file) not in ['None', '']:
21 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier)) 18 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
22 #set flye_version = $flye_version.rstrip('(assembly info)') 19 #set flye_version = $flye_version.rstrip('(assembly info)')
57 --amr_matrix_png_dir 'amr_matrix_png_dir' 54 --amr_matrix_png_dir 'amr_matrix_png_dir'
58 --amr_deletions_file '$amr_deletions_file' 55 --amr_deletions_file '$amr_deletions_file'
59 --analysis_name '$analysis_name' 56 --analysis_name '$analysis_name'
60 --assembly_fasta_file '$assembly_fasta_file' 57 --assembly_fasta_file '$assembly_fasta_file'
61 --assembly_name '$assembly_name' 58 --assembly_name '$assembly_name'
62 #if str($blastn_file) not in ['None', '']: 59 --blastn_version '$blastn_version'
63 --blastn_version '$blastn_version'
64 #end if
65 --compute_sequence_length_file '$compute_sequence_length_file' 60 --compute_sequence_length_file '$compute_sequence_length_file'
66 --contig_coverage_file '$contig_coverage_file' 61 --contig_coverage_file '$contig_coverage_file'
67 --dbkey '$aligned_sample.metadata.dbkey' 62 --dbkey '$aligned_sample.metadata.dbkey'
68 --dnadiff_snps_file '$dnadiff_snps_file' 63 --dnadiff_snps_file '$dnadiff_snps_file'
69 --dnadiff_version '$dnadiff_version' 64 --dnadiff_version '$dnadiff_version'