Mercurial > repos > greg > pima_report
comparison pima_report.xml @ 5:7177d81eb7cb draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Mar 2023 17:50:28 +0000 |
| parents | 428aed51c487 |
| children | 99613333fd1f |
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| 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' |