Mercurial > repos > greg > pima_report
diff 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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--- a/pima_report.xml Thu Mar 09 16:52:14 2023 +0000 +++ b/pima_report.xml Thu Mar 09 17:50:28 2023 +0000 @@ -10,11 +10,8 @@ #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier)) #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) -#set blastn_version = 'unknown' -#for $i in $blastn_features: - #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier)) -#end for - +#set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) +#set blastn_version = $blastn_version.rstrip('(features)') #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) #set dnadiff_version = $dnadiff_version.rstrip('(snps)') #if str($flye_assembly_info_file) not in ['None', '']: @@ -59,9 +56,7 @@ --analysis_name '$analysis_name' --assembly_fasta_file '$assembly_fasta_file' --assembly_name '$assembly_name' -#if str($blastn_file) not in ['None', '']: - --blastn_version '$blastn_version' -#end if +--blastn_version '$blastn_version' --compute_sequence_length_file '$compute_sequence_length_file' --contig_coverage_file '$contig_coverage_file' --dbkey '$aligned_sample.metadata.dbkey'