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comparison pima_report.xml @ 26:46edd7435555 draft

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author greg
date Tue, 25 Apr 2023 20:31:35 +0000
parents 4986a7fb2145
children 27485e70ed2b
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25:4986a7fb2145 26:46edd7435555
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 #if str($read_type) == 'ont': 10 #if str($read_type_cond.read_type) == 'ont':
11 #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier)) 11 #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.ont_file.element_identifier))
12 #else: 12 #else:
13 #set analysis_name = re.sub('[^\s\w\-]', '_', str($extracted_fastq_file.element_identifier)) 13 #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.illumina_forward_read.element_identifier))
14 #end if 14 #end if
15 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) 15 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
16 16
17 #if str($bedtools_complementbed_file) not in ['None', '']: 17 #if str($bedtools_complementbed_file) not in ['None', '']:
18 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier)) 18 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
21 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier)) 21 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
22 #end if 22 #end if
23 #if str($dnadiff_snps_file) not in ['None', '']: 23 #if str($dnadiff_snps_file) not in ['None', '']:
24 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) 24 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
25 #end if 25 #end if
26 #if str($assembler_version_file) not in ['None', '']: 26
27 ## All ONT samples are single-end reads, while all Illumina samples are
28 ## sets if paired reads. For ONT, we need both an assembly_fasta_file
29 ## which is produced by the medaka pipeline and and assembler_version_file
30 ## which is produced by flye. For Illumina we need only the assembly_fasta_file
31 ## which is produced by SPAdes since the version can be derived from it.
32 #if str($assembler_version_file) in ['None', '']:
33 ## We're analyzing a set of Illumina paired reads.
34 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
35 #else:
36 ## We're analyzing an ONT sample.
27 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier)) 37 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier))
28 #end if 38 #end if
39
29 #if str($kraken2_report_file) not in ['None', '']: 40 #if str($kraken2_report_file) not in ['None', '']:
30 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier)) 41 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
31 #end if 42 #end if
32 #if str($minimap2_bam_file) not in ['None', '']: 43 #if str($minimap2_bam_file) not in ['None', '']:
33 #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier)) 44 #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
95 --errors_file '$errors_file' 106 --errors_file '$errors_file'
96 --feature_bed_dir 'feature_bed_dir' 107 --feature_bed_dir 'feature_bed_dir'
97 --feature_png_dir 'feature_png_dir' 108 --feature_png_dir 'feature_png_dir'
98 #if str($assembler_version_file) not in ['None', '']: 109 #if str($assembler_version_file) not in ['None', '']:
99 --assembler_version '$assembler_version' 110 --assembler_version '$assembler_version'
100 #if str($read_type) == 'ont': 111 #if str($read_type_cond.read_type) == 'ont':
101 ## Need to pass the tabular flye assembly file. 112 ## Need to pass the tabular flye assembly file.
102 --flye_assembly_info_file '$assembler_version_file' 113 --flye_assembly_info_file '$assembler_version_file'
103 #end if 114 #end if
104 #end if 115 #end if
105 --genome_insertions_file '$genome_insertions_file' 116 --genome_insertions_file '$genome_insertions_file'
106 #if $fastq_file.ext.endswith(".gz"): 117 #if str($read_type_cond.read_type) == 'ont':
107 --gzipped 118 ## We're analyzing a single-edn ONT sample.
108 #end if 119 #if $read_type_cond.ont_file.ext.endswith(".gz"):
109 --fastq_file '$fastq_file' 120 --gzipped
121 #end if
122 --ont_file '$read_type_cond.ont_file'
123 #else:
124 ## We're analyzing a set of Illumina paired reads.
125 #if $read_type_cond.illumina_forward_read.ext.endswith(".gz"):
126 --gzipped
127 #end if
128 --illumina_forward_read_file '$read_type_cond.illumina_forward_read'
129 --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read'
130 #end if
110 #if str($kraken2_report_file) not in ['None', '']: 131 #if str($kraken2_report_file) not in ['None', '']:
111 --kraken2_report_file '$kraken2_report_file' 132 --kraken2_report_file '$kraken2_report_file'
112 --kraken2_version '$kraken2_version' 133 --kraken2_version '$kraken2_version'
113 #end if 134 #end if
114 #if str($minimap2_bam_file) not in ['None', '']: 135 #if str($minimap2_bam_file) not in ['None', '']:
117 --mutation_regions_dir 'mutation_regions_dir' 138 --mutation_regions_dir 'mutation_regions_dir'
118 --mutation_regions_bed_file '$mutation_regions_bed_file' 139 --mutation_regions_bed_file '$mutation_regions_bed_file'
119 --pima_css '${__tool_directory__}/pima.css' 140 --pima_css '${__tool_directory__}/pima.css'
120 --plasmids_file '$plasmids_file' 141 --plasmids_file '$plasmids_file'
121 --quast_report_file '$quast_report_file' 142 --quast_report_file '$quast_report_file'
122 --read_type '$read_type' 143 --read_type '$read_type_cond.read_type'
123 --reference_insertions_file '$reference_insertions_file' 144 --reference_insertions_file '$reference_insertions_file'
124 #if str($samtools_pileup_file) not in ['None', '']: 145 #if str($samtools_pileup_file) not in ['None', '']:
125 --samtools_version '$samtools_version' 146 --samtools_version '$samtools_version'
126 #end if 147 #end if
127 #if str($varscan_vcf_file) not in ['None', '']: 148 #if str($varscan_vcf_file) not in ['None', '']:
139 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/> 160 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
140 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 161 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
141 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 162 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
142 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 163 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
143 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/> 164 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
144 <param name="extracted_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Fastq sample file extracted from a paired collection" help="Used only with Illumina paired reads, leave blank to ignore"/>
145 <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
146 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 165 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
147 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 166 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
148 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> 167 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
149 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 168 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
150 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> 169 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
151 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> 170 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
152 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 171 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
153 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 172 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
154 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> 173 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
155 <param argument="--read_type" type="select" label="Specify the read type"> 174 <conditional name="read_type_cond">
156 <option value="ont" selected="true">Long reads - Oxford Nanopore Technologies (ONT)</option> 175 <param argument="--read_type" type="select" label="Specify the read type">
157 <option value="illumina">Short reads - Illumina</option> 176 <option value="ont" selected="true">ONT single read</option>
158 </param> 177 <option value="illumina">Illumina read pair</option>
178 </param>
179 <when value="ont">
180 <param name="ont_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT single read sample file"/>
181 </when>
182 <when value="illumina">
183 <param name="illumina_forward_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina forward read sample file"/>
184 <param name="illumina_reverse_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina reverse read sample file"/>
185 </when>
186 </conditional>
159 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> 187 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
160 <param name="plasmids_file" type="data" format="tsv" optional="true" label="pChunks plasmids TSV file" help="Optional, ignored if not selected"/> 188 <param name="plasmids_file" type="data" format="tsv" optional="true" label="pChunks plasmids TSV file" help="Optional, ignored if not selected"/>
161 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> 189 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
162 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/> 190 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
163 </inputs> 191 </inputs>
167 <tests> 195 <tests>
168 <test> 196 <test>
169 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/> 197 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
170 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/> 198 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
171 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/> 199 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
172 <param name="fastq_file" value="ont_fastq.fastq" ftype="fastq"/> 200 <param name="read_type" value="ont"/>
201 <param name="ont_file" value="ont_fastq.fastq" ftype="fastq"/>
173 <output name="output" value="output.pdf" ftype="pdf"/> 202 <output name="output" value="output.pdf" ftype="pdf"/>
174 </test> 203 </test>
175 </tests> 204 </tests>
176 <help> 205 <help>
177 **What it does** 206 **What it does**