changeset 25:4986a7fb2145 draft

Uploaded

--- a/pima_report.py	Thu Apr 20 18:10:58 2023 +0000
+++ b/pima_report.py	Thu Apr 20 18:47:01 2023 +0000
@@ -542,7 +542,7 @@
                 contig_title = 'Alignment to %s' % contig
                 self.doc.new_line()
                 self.doc.new_header(level=3, title=contig_title)
-                self.doc.new_line('Blue indicates aligned sequences (to the reference) and yellow indicates missing sequences')
+                self.doc.new_line('Blue color indicates query sequences aligned to the reference sequence, which is shown in yellow')
                 self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(circos_file)))
                 self.doc.new_line('<div style="page-break-after: always;"></div>')
                 self.doc.new_line()
@@ -714,7 +714,7 @@
             amr_deletions = amr_deletions.loc[amr_deletions['type'].isin(['large-deletion', 'any']), :]
         self.doc.new_line()
         self.doc.new_header(level=2, title=self.large_indel_title)
-        self.doc.new_line('This section is informative only when your idolates were identified as *Bacillus anthracis* strains')
+        self.doc.new_line('This section is informative only when your isolates were identified as *Bacillus anthracis* strains')
         for genome in ['Reference insertions', 'Query insertions']:
             genome_indels = large_indels[genome].copy()
             self.doc.new_line()

--- a/pima_report.xml	Thu Apr 20 18:10:58 2023 +0000
+++ b/pima_report.xml	Thu Apr 20 18:47:01 2023 +0000
@@ -7,7 +7,11 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 
-#set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
+#if str($read_type) == 'ont':
+    #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
+#else:
+    #set analysis_name = re.sub('[^\s\w\-]', '_', str($extracted_fastq_file.element_identifier))
+#end if
 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
 
 #if str($bedtools_complementbed_file) not in ['None', '']:
@@ -137,6 +141,7 @@
         <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"/>
         <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
+        <param name="extracted_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Fastq sample file extracted from a paired collection" help="Used only with Illumina paired reads, leave blank to ignore"/>
         <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
         <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
         <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>