diff pima_report.xml @ 21:667b253329c6 draft

Uploaded
author greg
date Thu, 13 Apr 2023 17:13:40 +0000
parents e948214a9e3c
children d89b7d47a85a
line wrap: on
line diff
--- a/pima_report.xml	Thu Mar 30 20:41:18 2023 +0000
+++ b/pima_report.xml	Thu Apr 13 17:13:40 2023 +0000
@@ -7,7 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 
-#set analysis_name = re.sub('[^\s\w\-]', '_', str($ont_fastq_file.element_identifier))
+#set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
 
 #if str($bedtools_complementbed_file) not in ['None', '']:
@@ -19,8 +19,8 @@
 #if str($dnadiff_snps_file) not in ['None', '']:
     #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
 #end if
-#if str($flye_assembly_info_file) not in ['None', '']:
-    #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
+#if str($assembler_version_file) not in ['None', '']:
+    #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier))
 #end if
 #if str($kraken2_report_file) not in ['None', '']:
     #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
@@ -91,15 +91,18 @@
 --errors_file '$errors_file'
 --feature_bed_dir 'feature_bed_dir'
 --feature_png_dir 'feature_png_dir'
-#if str($flye_assembly_info_file) not in ['None', '']:
-    --flye_assembly_info_file '$flye_assembly_info_file'
-    --flye_version '$flye_version'
+#if str($assembler_version_file) not in ['None', '']:
+    --assembler_version '$assembler_version'
+    #if str($read_type) == 'ont':
+        ## Need to pass the tabular flye assembly file.
+        --flye_assembly_info_file '$assembler_version_file'
+    #end if
 #end if
 --genome_insertions_file '$genome_insertions_file'
-#if $ont_fastq_file.ext.endswith(".gz"):
+#if $fastq_file.ext.endswith(".gz"):
     --gzipped
 #end if
---ont_fastq_file '$ont_fastq_file'
+--fastq_file '$fastq_file'
 #if str($kraken2_report_file) not in ['None', '']:
     --kraken2_report_file '$kraken2_report_file'
     --kraken2_version '$kraken2_version'
@@ -134,12 +137,12 @@
         <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="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"/>
-        <param name="flye_assembly_info_file" type="data" format="tabular,tsv" optional="true" label="Flye assembly info tabular file" help="Optional, ignored if not selected"/>
+        <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
         <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
         <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
-        <param name="ont_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT fastq sample file"/>
         <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
         <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
         <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
@@ -161,7 +164,7 @@
             <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
             <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
             <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
-            <param name="ont_fastq_file" value="ont_fastq.fastq" ftype="fastq"/>
+            <param name="fastq_file" value="ont_fastq.fastq" ftype="fastq"/>
             <output name="output" value="output.pdf" ftype="pdf"/>
         </test>
     </tests>