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comparison pima_report.xml @ 12:99613333fd1f draft

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Uploaded
author greg
date Fri, 10 Mar 2023 16:35:16 +0000
parents 7177d81eb7cb
children f03c80bb22e9
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11:4a7c31f28197 12:99613333fd1f
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 12
13 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) 13 #if str($bedtools_complementbed_file) not in ['None', '']:
14 #set blastn_version = $blastn_version.rstrip('(features)') 14 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
15 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) 15 #end if
16 #set dnadiff_version = $dnadiff_version.rstrip('(snps)') 16 #if str($blastn_features) not in ['None', '']:
17 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
18 #end if
19 #if str($dnadiff_snps_file) not in ['None', '']:
20 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
21 #end if
17 #if str($flye_assembly_info_file) not in ['None', '']: 22 #if str($flye_assembly_info_file) not in ['None', '']:
18 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier)) 23 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
19 #set flye_version = $flye_version.rstrip('(assembly info)')
20 #end if 24 #end if
21 #if str($kraken2_report_file) not in ['None', '']: 25 #if str($kraken2_report_file) not in ['None', '']:
22 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier)) 26 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
23 #set kraken2_version = $kraken2_version.rstrip('(report)') 27 #end if
28 #if str($minimap2_bam_file) not in ['None', '']:
29 #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
30 #end if
31 #if str($samtools_pileup_file) not in ['None', '']:
32 #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier))
33 #end if
34 #if str($varscan_vcf_file) not in ['None', '']:
35 #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
24 #end if 36 #end if
25 37
26 mkdir amr_matrix_png_dir && 38 mkdir amr_matrix_png_dir &&
27 mkdir feature_bed_dir && 39 mkdir feature_bed_dir &&
28 mkdir feature_png_dir && 40 mkdir feature_png_dir &&
54 --amr_matrix_png_dir 'amr_matrix_png_dir' 66 --amr_matrix_png_dir 'amr_matrix_png_dir'
55 --amr_deletions_file '$amr_deletions_file' 67 --amr_deletions_file '$amr_deletions_file'
56 --analysis_name '$analysis_name' 68 --analysis_name '$analysis_name'
57 --assembly_fasta_file '$assembly_fasta_file' 69 --assembly_fasta_file '$assembly_fasta_file'
58 --assembly_name '$assembly_name' 70 --assembly_name '$assembly_name'
59 --blastn_version '$blastn_version' 71 #if str($bedtools_complementbed_file) not in ['None', '']:
72 --bedtools_version '$bedtools_version'
73 #end if
74 #if str($blastn_features) not in ['None', '']:
75 --blastn_version '$blastn_version'
76 #end if
60 --compute_sequence_length_file '$compute_sequence_length_file' 77 --compute_sequence_length_file '$compute_sequence_length_file'
61 --contig_coverage_file '$contig_coverage_file' 78 --contig_coverage_file '$contig_coverage_file'
62 --dbkey '$aligned_sample.metadata.dbkey' 79 --dbkey '$aligned_sample.metadata.dbkey'
63 --dnadiff_snps_file '$dnadiff_snps_file' 80 --dnadiff_snps_file '$dnadiff_snps_file'
64 --dnadiff_version '$dnadiff_version' 81 #if str($dnadiff_snps_file) not in ['None', '']:
82 --dnadiff_version '$dnadiff_version'
83 #end if
65 --feature_bed_dir 'feature_bed_dir' 84 --feature_bed_dir 'feature_bed_dir'
66 --feature_png_dir 'feature_png_dir' 85 --feature_png_dir 'feature_png_dir'
67 #if str($flye_assembly_info_file) not in ['None', '']: 86 #if str($flye_assembly_info_file) not in ['None', '']:
68 --flye_assembly_info_file '$flye_assembly_info_file' 87 --flye_assembly_info_file '$flye_assembly_info_file'
69 --flye_version '$flye_version' 88 --flye_version '$flye_version'
75 --illumina_fastq_file '$illumina_fastq_file' 94 --illumina_fastq_file '$illumina_fastq_file'
76 #if str($kraken2_report_file) not in ['None', '']: 95 #if str($kraken2_report_file) not in ['None', '']:
77 --kraken2_report_file '$kraken2_report_file' 96 --kraken2_report_file '$kraken2_report_file'
78 --kraken2_version '$kraken2_version' 97 --kraken2_version '$kraken2_version'
79 #end if 98 #end if
99 #if str($minimap2_bam_file) not in ['None', '']:
100 --minimap2_version '$minimap2_version'
101 #end if
80 --mutation_regions_dir 'mutation_regions_dir' 102 --mutation_regions_dir 'mutation_regions_dir'
81 --mutation_regions_bed_file '$mutation_regions_bed_file' 103 --mutation_regions_bed_file '$mutation_regions_bed_file'
82 --pima_css '${__tool_directory__}/pima.css' 104 --pima_css '${__tool_directory__}/pima.css'
83 --plasmids_file '$plasmids_file' 105 --plasmids_file '$plasmids_file'
84 --reference_insertions_file '$reference_insertions_file' 106 --reference_insertions_file '$reference_insertions_file'
107 #if str($samtools_pileup_file) not in ['None', '']:
108 --samtools_version '$samtools_version'
109 #end if
110 #if str($varscan_vcf_file) not in ['None', '']:
111 --varscan_version '$varscan_version'
112 #end if
85 && mv 'pima_report.pdf' '$output' 113 && mv 'pima_report.pdf' '$output'
86 ]]></command> 114 ]]></command>
87 <inputs> 115 <inputs>
88 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/> 116 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
89 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/> 117 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
90 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/> 118 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
91 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/> 119 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
120 <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
92 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/> 121 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
93 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 122 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
94 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 123 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
95 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 124 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
96 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 125 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
97 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 126 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
98 <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"/> 127 <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"/>
99 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 128 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
100 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> 129 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
101 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 130 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
131 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
102 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 132 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
103 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 133 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
104 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> 134 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
105 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> 135 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
136 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
137 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
106 </inputs> 138 </inputs>
107 <outputs> 139 <outputs>
108 <data name="output" format="pdf"/> 140 <data name="output" format="pdf"/>
109 </outputs> 141 </outputs>
110 <tests> 142 <tests>