Mercurial > repos > greg > pima_report
view pima_report.xml @ 21:667b253329c6 draft
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author | greg |
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date | Thu, 13 Apr 2023 17:13:40 +0000 |
parents | e948214a9e3c |
children | d89b7d47a85a |
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<tool id="pima_report" name="PIMA: summary report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import re #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($bedtools_complementbed_file) not in ['None', '']: #set bedtools_version = re.sub('[^\s\w\-]', '_', str($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($assembler_version_file) not in ['None', '']: #set assembler_version = re.sub('[^\s\w\-]', '_', str($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)) #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 && mkdir circos_png_dir && mkdir feature_bed_dir && mkdir feature_png_dir && mkdir mutation_regions_dir && touch 'pima_report.pdf' && #for $i in $amr_matrices_png: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s $i 'amr_matrix_png_dir/$identifier' && #end for #for $i in $circos_png: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s $i 'circos_png_dir/$identifier' && #end for #for $i in $features_bed: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s $i 'feature_bed_dir/$identifier' && #end for #for $i in $features_png: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s $i 'feature_png_dir/$identifier' && #end for #for $i in $mutation_regions: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s $i 'mutation_regions_dir/$identifier' && #end for python '${__tool_directory__}/pima_report.py' --amr_matrix_png_dir 'amr_matrix_png_dir' --amr_deletions_file '$amr_deletions_file' --analysis_name '$analysis_name' --assembly_fasta_file '$assembly_fasta_file' --assembly_name '$assembly_name' #if str($bedtools_complementbed_file) not in ['None', '']: --bedtools_version '$bedtools_version' #end if #if str($blastn_features) not in ['None', '']: --blastn_version '$blastn_version' #end if --circos_png_dir 'circos_png_dir' --compute_sequence_length_file '$compute_sequence_length_file' --contig_coverage_file '$contig_coverage_file' --dbkey '$aligned_sample.metadata.dbkey' --dnadiff_snps_file '$dnadiff_snps_file' #if str($dnadiff_snps_file) not in ['None', '']: --dnadiff_version '$dnadiff_version' #end if --errors_file '$errors_file' --feature_bed_dir 'feature_bed_dir' --feature_png_dir 'feature_png_dir' #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 $fastq_file.ext.endswith(".gz"): --gzipped #end if --fastq_file '$fastq_file' #if str($kraken2_report_file) not in ['None', '']: --kraken2_report_file '$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' --quast_report_file '$quast_report_file' --read_type '$read_type' --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> <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/> <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="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG 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"/> <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="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="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="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> <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"/> </outputs> <tests> <test> <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"/> <output name="output" value="output.pdf" ftype="pdf"/> </test> </tests> <help> **What it does** Generates the PIMA analysis summary report. </help> <expand macro="citations"/> </tool>