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**