Mercurial > repos > greg > pima_report
diff pima_report.xml @ 26:46edd7435555 draft
Uploaded
author | greg |
---|---|
date | Tue, 25 Apr 2023 20:31:35 +0000 |
parents | 4986a7fb2145 |
children | 27485e70ed2b |
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--- a/pima_report.xml Thu Apr 20 18:47:01 2023 +0000 +++ b/pima_report.xml Tue Apr 25 20:31:35 2023 +0000 @@ -7,10 +7,10 @@ <command detect_errors="exit_code"><![CDATA[ #import re -#if str($read_type) == 'ont': - #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier)) +#if str($read_type_cond.read_type) == 'ont': + #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.ont_file.element_identifier)) #else: - #set analysis_name = re.sub('[^\s\w\-]', '_', str($extracted_fastq_file.element_identifier)) + #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.illumina_forward_read.element_identifier)) #end if #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) @@ -23,9 +23,20 @@ #if str($dnadiff_snps_file) not in ['None', '']: #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) #end if -#if str($assembler_version_file) not in ['None', '']: + +## All ONT samples are single-end reads, while all Illumina samples are +## sets if paired reads. For ONT, we need both an assembly_fasta_file +## which is produced by the medaka pipeline and and assembler_version_file +## which is produced by flye. For Illumina we need only the assembly_fasta_file +## which is produced by SPAdes since the version can be derived from it. +#if str($assembler_version_file) in ['None', '']: + ## We're analyzing a set of Illumina paired reads. + #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) +#else: + ## We're analyzing an ONT sample. #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($kraken2_report_file.element_identifier)) #end if @@ -97,16 +108,26 @@ --feature_png_dir 'feature_png_dir' #if str($assembler_version_file) not in ['None', '']: --assembler_version '$assembler_version' - #if str($read_type) == 'ont': + #if str($read_type_cond.read_type) == 'ont': ## Need to pass the tabular flye assembly file. --flye_assembly_info_file '$assembler_version_file' #end if #end if --genome_insertions_file '$genome_insertions_file' -#if $fastq_file.ext.endswith(".gz"): - --gzipped +#if str($read_type_cond.read_type) == 'ont': + ## We're analyzing a single-edn ONT sample. + #if $read_type_cond.ont_file.ext.endswith(".gz"): + --gzipped + #end if + --ont_file '$read_type_cond.ont_file' +#else: + ## We're analyzing a set of Illumina paired reads. + #if $read_type_cond.illumina_forward_read.ext.endswith(".gz"): + --gzipped + #end if + --illumina_forward_read_file '$read_type_cond.illumina_forward_read' + --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read' #end if ---fastq_file '$fastq_file' #if str($kraken2_report_file) not in ['None', '']: --kraken2_report_file '$kraken2_report_file' --kraken2_version '$kraken2_version' @@ -119,7 +140,7 @@ --pima_css '${__tool_directory__}/pima.css' --plasmids_file '$plasmids_file' --quast_report_file '$quast_report_file' ---read_type '$read_type' +--read_type '$read_type_cond.read_type' --reference_insertions_file '$reference_insertions_file' #if str($samtools_pileup_file) not in ['None', '']: --samtools_version '$samtools_version' @@ -141,8 +162,6 @@ <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"/> <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> @@ -152,10 +171,19 @@ <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"/> <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> - <param argument="--read_type" type="select" label="Specify the read type"> - <option value="ont" selected="true">Long reads - Oxford Nanopore Technologies (ONT)</option> - <option value="illumina">Short reads - Illumina</option> - </param> + <conditional name="read_type_cond"> + <param argument="--read_type" type="select" label="Specify the read type"> + <option value="ont" selected="true">ONT single read</option> + <option value="illumina">Illumina read pair</option> + </param> + <when value="ont"> + <param name="ont_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT single read sample file"/> + </when> + <when value="illumina"> + <param name="illumina_forward_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina forward read sample file"/> + <param name="illumina_reverse_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina reverse read sample file"/> + </when> + </conditional> <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> <param name="plasmids_file" type="data" format="tsv" optional="true" label="pChunks plasmids TSV file" help="Optional, ignored if not selected"/> <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> @@ -169,7 +197,8 @@ <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="fastq_file" value="ont_fastq.fastq" ftype="fastq"/> + <param name="read_type" value="ont"/> + <param name="ont_file" value="ont_fastq.fastq" ftype="fastq"/> <output name="output" value="output.pdf" ftype="pdf"/> </test> </tests>