Mercurial > repos > greg > pima_report
diff pima_report.xml @ 21:667b253329c6 draft
Uploaded
author | greg |
---|---|
date | Thu, 13 Apr 2023 17:13:40 +0000 |
parents | e948214a9e3c |
children | d89b7d47a85a |
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--- 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>