Mercurial > repos > greg > pima_report

changeset 3:33d9832420c5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 09 Mar 2023 16:44:59 +0000
parents 9cb62054a87a
children 428aed51c487
files pima_report.xml
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/pima_report.xml	Thu Mar 09 16:26:29 2023 +0000
+++ b/pima_report.xml	Thu Mar 09 16:44:59 2023 +0000
@@ -10,9 +10,11 @@
 #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))
 
-#if str($blastn_file) not in ['None', '']:
+#set blastn_version = 'unknown'
+#for $i in $blastn_features:
     #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
-#end if
+#end for
+
 #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', '']:
@@ -92,7 +94,7 @@
         <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
         <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
         <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
-        <param name="blastn_file" type="data" format="bam" label="Blastn BAM file"/>
+        <param name="blastn_features" format="bam" type="data_collection" collection_type="list" label="Collection of blastn BAM files"/>
         <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
         <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
         <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>