comparison pima_report.xml @ 2:9cb62054a87a draft

Uploaded
author greg
date Thu, 09 Mar 2023 16:26:29 +0000
parents 67d0939b56b0
children 33d9832420c5
comparison
equal deleted inserted replaced
1:67d0939b56b0 2:9cb62054a87a
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re 8 #import re
9 9
10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier)) 10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) 11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
12
13 #if str($blastn_file) not in ['None', '']:
14 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
15 #end if
16 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
17 #set dnadiff_version = $dnadiff_version.rstrip('(snps)')
12 #if str($flye_assembly_info_file) not in ['None', '']: 18 #if str($flye_assembly_info_file) not in ['None', '']:
13 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier)) 19 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
14 #set flye_version = $flye_version.rstrip('(assembly info)') 20 #set flye_version = $flye_version.rstrip('(assembly info)')
21 #end if
22 #if str($kraken2_report_file) not in ['None', '']:
23 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
24 #set kraken2_version = $kraken2_version.rstrip('(report)')
15 #end if 25 #end if
16 26
17 mkdir amr_matrix_png_dir && 27 mkdir amr_matrix_png_dir &&
18 mkdir feature_bed_dir && 28 mkdir feature_bed_dir &&
19 mkdir feature_png_dir && 29 mkdir feature_png_dir &&
45 --amr_matrix_png_dir 'amr_matrix_png_dir' 55 --amr_matrix_png_dir 'amr_matrix_png_dir'
46 --amr_deletions_file '$amr_deletions_file' 56 --amr_deletions_file '$amr_deletions_file'
47 --analysis_name '$analysis_name' 57 --analysis_name '$analysis_name'
48 --assembly_fasta_file '$assembly_fasta_file' 58 --assembly_fasta_file '$assembly_fasta_file'
49 --assembly_name '$assembly_name' 59 --assembly_name '$assembly_name'
60 #if str($blastn_file) not in ['None', '']:
61 --blastn_version '$blastn_version'
62 #end if
50 --compute_sequence_length_file '$compute_sequence_length_file' 63 --compute_sequence_length_file '$compute_sequence_length_file'
51 --contig_coverage_file '$contig_coverage_file' 64 --contig_coverage_file '$contig_coverage_file'
52 --dbkey '$aligned_sample.metadata.dbkey' 65 --dbkey '$aligned_sample.metadata.dbkey'
53 --dnadiff_snps_file '$dnadiff_snps_file' 66 --dnadiff_snps_file '$dnadiff_snps_file'
67 --dnadiff_version '$dnadiff_version'
54 --feature_bed_dir 'feature_bed_dir' 68 --feature_bed_dir 'feature_bed_dir'
55 --feature_png_dir 'feature_png_dir' 69 --feature_png_dir 'feature_png_dir'
56 #if str($flye_assembly_info_file) not in ['None', '']: 70 #if str($flye_assembly_info_file) not in ['None', '']:
57 --flye_assembly_info_file '$flye_assembly_info_file' 71 --flye_assembly_info_file '$flye_assembly_info_file'
58 --flye_version '$flye_version' 72 --flye_version '$flye_version'
60 --genome_insertions_file '$genome_insertions_file' 74 --genome_insertions_file '$genome_insertions_file'
61 #if $illumina_fastq_file.ext.endswith(".gz"): 75 #if $illumina_fastq_file.ext.endswith(".gz"):
62 --gzipped 76 --gzipped
63 #end if 77 #end if
64 --illumina_fastq_file '$illumina_fastq_file' 78 --illumina_fastq_file '$illumina_fastq_file'
79 #if str($kraken2_report_file) not in ['None', '']:
80 --kraken2_report_file '$kraken2_report_file'
81 --kraken2_version '$kraken2_version'
82 #end if
65 --mutation_regions_dir 'mutation_regions_dir' 83 --mutation_regions_dir 'mutation_regions_dir'
66 --mutation_regions_bed_file '$mutation_regions_bed_file' 84 --mutation_regions_bed_file '$mutation_regions_bed_file'
67 --pima_css '${__tool_directory__}/pima.css' 85 --pima_css '${__tool_directory__}/pima.css'
68 --plasmids_file '$plasmids_file' 86 --plasmids_file '$plasmids_file'
69 --reference_insertions_file '$reference_insertions_file' 87 --reference_insertions_file '$reference_insertions_file'
72 <inputs> 90 <inputs>
73 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/> 91 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
74 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/> 92 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
75 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/> 93 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
76 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/> 94 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
95 <param name="blastn_file" type="data" format="bam" label="Blastn BAM file"/>
77 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 96 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
78 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 97 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
79 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 98 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
80 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 99 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
81 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 100 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
82 <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"/> 101 <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"/>
83 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 102 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
103 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
84 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 104 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
85 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 105 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
86 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 106 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
87 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> 107 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
88 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> 108 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>