Mercurial > repos > greg > pima_report
comparison pima_report.xml @ 21:667b253329c6 draft
Uploaded
author | greg |
---|---|
date | Thu, 13 Apr 2023 17:13:40 +0000 |
parents | e948214a9e3c |
children | d89b7d47a85a |
comparison
equal
deleted
inserted
replaced
20:4fe8c35cd176 | 21:667b253329c6 |
---|---|
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
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($ont_fastq_file.element_identifier)) | 10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($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 #if str($bedtools_complementbed_file) not in ['None', '']: | 13 #if str($bedtools_complementbed_file) not in ['None', '']: |
14 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier)) | 14 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier)) |
15 #end if | 15 #end if |
17 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) | 17 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) |
18 #end if | 18 #end if |
19 #if str($dnadiff_snps_file) not in ['None', '']: | 19 #if str($dnadiff_snps_file) not in ['None', '']: |
20 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) | 20 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) |
21 #end if | 21 #end if |
22 #if str($flye_assembly_info_file) not in ['None', '']: | 22 #if str($assembler_version_file) not in ['None', '']: |
23 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier)) | 23 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier)) |
24 #end if | 24 #end if |
25 #if str($kraken2_report_file) not in ['None', '']: | 25 #if str($kraken2_report_file) not in ['None', '']: |
26 #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)) |
27 #end if | 27 #end if |
28 #if str($minimap2_bam_file) not in ['None', '']: | 28 #if str($minimap2_bam_file) not in ['None', '']: |
89 --dnadiff_version '$dnadiff_version' | 89 --dnadiff_version '$dnadiff_version' |
90 #end if | 90 #end if |
91 --errors_file '$errors_file' | 91 --errors_file '$errors_file' |
92 --feature_bed_dir 'feature_bed_dir' | 92 --feature_bed_dir 'feature_bed_dir' |
93 --feature_png_dir 'feature_png_dir' | 93 --feature_png_dir 'feature_png_dir' |
94 #if str($flye_assembly_info_file) not in ['None', '']: | 94 #if str($assembler_version_file) not in ['None', '']: |
95 --flye_assembly_info_file '$flye_assembly_info_file' | 95 --assembler_version '$assembler_version' |
96 --flye_version '$flye_version' | 96 #if str($read_type) == 'ont': |
97 ## Need to pass the tabular flye assembly file. | |
98 --flye_assembly_info_file '$assembler_version_file' | |
99 #end if | |
97 #end if | 100 #end if |
98 --genome_insertions_file '$genome_insertions_file' | 101 --genome_insertions_file '$genome_insertions_file' |
99 #if $ont_fastq_file.ext.endswith(".gz"): | 102 #if $fastq_file.ext.endswith(".gz"): |
100 --gzipped | 103 --gzipped |
101 #end if | 104 #end if |
102 --ont_fastq_file '$ont_fastq_file' | 105 --fastq_file '$fastq_file' |
103 #if str($kraken2_report_file) not in ['None', '']: | 106 #if str($kraken2_report_file) not in ['None', '']: |
104 --kraken2_report_file '$kraken2_report_file' | 107 --kraken2_report_file '$kraken2_report_file' |
105 --kraken2_version '$kraken2_version' | 108 --kraken2_version '$kraken2_version' |
106 #end if | 109 #end if |
107 #if str($minimap2_bam_file) not in ['None', '']: | 110 #if str($minimap2_bam_file) not in ['None', '']: |
132 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/> | 135 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/> |
133 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> | 136 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> |
134 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> | 137 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> |
135 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> | 138 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> |
136 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/> | 139 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/> |
140 <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> | |
137 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> | 141 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> |
138 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> | 142 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> |
139 <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"/> | 143 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> |
140 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> | 144 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> |
141 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> | 145 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> |
142 <param name="ont_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT fastq sample file"/> | |
143 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> | 146 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> |
144 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> | 147 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> |
145 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> | 148 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> |
146 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> | 149 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> |
147 <param argument="--read_type" type="select" label="Specify the read type"> | 150 <param argument="--read_type" type="select" label="Specify the read type"> |
159 <tests> | 162 <tests> |
160 <test> | 163 <test> |
161 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/> | 164 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/> |
162 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/> | 165 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/> |
163 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/> | 166 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/> |
164 <param name="ont_fastq_file" value="ont_fastq.fastq" ftype="fastq"/> | 167 <param name="fastq_file" value="ont_fastq.fastq" ftype="fastq"/> |
165 <output name="output" value="output.pdf" ftype="pdf"/> | 168 <output name="output" value="output.pdf" ftype="pdf"/> |
166 </test> | 169 </test> |
167 </tests> | 170 </tests> |
168 <help> | 171 <help> |
169 **What it does** | 172 **What it does** |