Mercurial > repos > greg > pima_report
diff pima_report.xml @ 12:99613333fd1f draft
Uploaded
author | greg |
---|---|
date | Fri, 10 Mar 2023 16:35:16 +0000 |
parents | 7177d81eb7cb |
children | f03c80bb22e9 |
line wrap: on
line diff
--- a/pima_report.xml Thu Mar 09 18:34:01 2023 +0000 +++ b/pima_report.xml Fri Mar 10 16:35:16 2023 +0000 @@ -10,17 +10,29 @@ #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)) -#set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) -#set blastn_version = $blastn_version.rstrip('(features)') -#set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) -#set dnadiff_version = $dnadiff_version.rstrip('(snps)') +#if str($bedtools_complementbed_file) not in ['None', '']: + #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier)) +#end if +#if str($blastn_features) not in ['None', '']: + #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) +#end if +#if str($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)) - #set flye_version = $flye_version.rstrip('(assembly info)') #end if #if str($kraken2_report_file) not in ['None', '']: #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier)) - #set kraken2_version = $kraken2_version.rstrip('(report)') +#end if +#if str($minimap2_bam_file) not in ['None', '']: + #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier)) +#end if +#if str($samtools_pileup_file) not in ['None', '']: + #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier)) +#end if +#if str($varscan_vcf_file) not in ['None', '']: + #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier)) #end if mkdir amr_matrix_png_dir && @@ -56,12 +68,19 @@ --analysis_name '$analysis_name' --assembly_fasta_file '$assembly_fasta_file' --assembly_name '$assembly_name' ---blastn_version '$blastn_version' +#if str($bedtools_complementbed_file) not in ['None', '']: + --bedtools_version '$bedtools_version' +#end if +#if str($blastn_features) not in ['None', '']: + --blastn_version '$blastn_version' +#end if --compute_sequence_length_file '$compute_sequence_length_file' --contig_coverage_file '$contig_coverage_file' --dbkey '$aligned_sample.metadata.dbkey' --dnadiff_snps_file '$dnadiff_snps_file' ---dnadiff_version '$dnadiff_version' +#if str($dnadiff_snps_file) not in ['None', '']: + --dnadiff_version '$dnadiff_version' +#end if --feature_bed_dir 'feature_bed_dir' --feature_png_dir 'feature_png_dir' #if str($flye_assembly_info_file) not in ['None', '']: @@ -77,11 +96,20 @@ --kraken2_report_file '$kraken2_report_file' --kraken2_version '$kraken2_version' #end if +#if str($minimap2_bam_file) not in ['None', '']: + --minimap2_version '$minimap2_version' +#end if --mutation_regions_dir 'mutation_regions_dir' --mutation_regions_bed_file '$mutation_regions_bed_file' --pima_css '${__tool_directory__}/pima.css' --plasmids_file '$plasmids_file' --reference_insertions_file '$reference_insertions_file' +#if str($samtools_pileup_file) not in ['None', '']: + --samtools_version '$samtools_version' +#end if +#if str($varscan_vcf_file) not in ['None', '']: + --varscan_version '$varscan_version' +#end if && mv 'pima_report.pdf' '$output' ]]></command> <inputs> @@ -89,6 +117,7 @@ <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="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/> <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular 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"/> @@ -99,10 +128,13 @@ <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="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="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"/> <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> + <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> + <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/> </inputs> <outputs> <data name="output" format="pdf"/>