Mercurial > repos > greg > pima_report
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> |