comparison pima_report.xml @ 1:67d0939b56b0 draft

Uploaded
author greg
date Tue, 07 Mar 2023 16:05:14 +0000
parents 0a558f444c98
children 9cb62054a87a
comparison
equal deleted inserted replaced
0:0a558f444c98 1:67d0939b56b0
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 #if str($flye_assembly_info_file) not in ['None', '']:
13 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
14 #set flye_version = $flye_version.rstrip('(assembly info)')
15 #end if
12 16
17 mkdir amr_matrix_png_dir &&
13 mkdir feature_bed_dir && 18 mkdir feature_bed_dir &&
14 mkdir feature_png_dir && 19 mkdir feature_png_dir &&
15 mkdir mutation_regions_dir && 20 mkdir mutation_regions_dir &&
16 touch 'pima_report.pdf' && 21 touch 'pima_report.pdf' &&
17 22
23 #for $i in $amr_matrices_png:
24 #set file_name = $i.file_name
25 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
26 ln -s $i 'amr_matrix_png_dir/$identifier' &&
27 #end for
18 #for $i in $features_bed: 28 #for $i in $features_bed:
19 #set file_name = $i.file_name 29 #set file_name = $i.file_name
20 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 30 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
21 ln -s $i 'feature_bed_dir/$identifier' && 31 ln -s $i 'feature_bed_dir/$identifier' &&
22 #end for 32 #end for
30 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 40 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
31 ln -s $i 'mutation_regions_dir/$identifier' && 41 ln -s $i 'mutation_regions_dir/$identifier' &&
32 #end for 42 #end for
33 43
34 python '${__tool_directory__}/pima_report.py' 44 python '${__tool_directory__}/pima_report.py'
45 --amr_matrix_png_dir 'amr_matrix_png_dir'
46 --amr_deletions_file '$amr_deletions_file'
35 --analysis_name '$analysis_name' 47 --analysis_name '$analysis_name'
36 --assembly_fasta_file '$assembly_fasta_file' 48 --assembly_fasta_file '$assembly_fasta_file'
37 --assembly_name '$assembly_name' 49 --assembly_name '$assembly_name'
50 --compute_sequence_length_file '$compute_sequence_length_file'
38 --contig_coverage_file '$contig_coverage_file' 51 --contig_coverage_file '$contig_coverage_file'
39 --dbkey '$aligned_sample.metadata.dbkey' 52 --dbkey '$aligned_sample.metadata.dbkey'
53 --dnadiff_snps_file '$dnadiff_snps_file'
40 --feature_bed_dir 'feature_bed_dir' 54 --feature_bed_dir 'feature_bed_dir'
41 --feature_png_dir 'feature_png_dir' 55 --feature_png_dir 'feature_png_dir'
56 #if str($flye_assembly_info_file) not in ['None', '']:
57 --flye_assembly_info_file '$flye_assembly_info_file'
58 --flye_version '$flye_version'
59 #end if
60 --genome_insertions_file '$genome_insertions_file'
42 #if $illumina_fastq_file.ext.endswith(".gz"): 61 #if $illumina_fastq_file.ext.endswith(".gz"):
43 --gzipped 62 --gzipped
44 #end if 63 #end if
45 --illumina_fastq_file '$illumina_fastq_file' 64 --illumina_fastq_file '$illumina_fastq_file'
46 --mutation_regions_dir 'mutation_regions_dir' 65 --mutation_regions_dir 'mutation_regions_dir'
47 --mutation_regions_bed_file '$mutation_regions_bed_file' 66 --mutation_regions_bed_file '$mutation_regions_bed_file'
48 --pima_css '${__tool_directory__}/pima.css' 67 --pima_css '${__tool_directory__}/pima.css'
68 --plasmids_file '$plasmids_file'
69 --reference_insertions_file '$reference_insertions_file'
49 && mv 'pima_report.pdf' '$output' 70 && mv 'pima_report.pdf' '$output'
50 ]]></command> 71 ]]></command>
51 <inputs> 72 <inputs>
73 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
52 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/> 74 <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"/>
53 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/> 76 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
77 <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"/>
79 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
54 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 80 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
55 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 81 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
56 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 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"/>
83 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
57 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 84 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
58 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 85 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
59 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 86 <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"/>
88 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
60 </inputs> 89 </inputs>
61 <outputs> 90 <outputs>
62 <data name="output" format="pdf"/> 91 <data name="output" format="pdf"/>
63 </outputs> 92 </outputs>
64 <tests> 93 <tests>