Mercurial > repos > greg > pima_report

comparison pima_report.xml @ 14:95b1d1a9497d draft

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Uploaded
author greg
date Fri, 17 Mar 2023 17:23:43 +0000
parents f03c80bb22e9
children e948214a9e3c
comparison
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13:f03c80bb22e9 14:95b1d1a9497d
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($illumina_fastq_file.element_identifier)) 10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($ont_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
93 #if str($flye_assembly_info_file) not in ['None', '']: 93 #if str($flye_assembly_info_file) not in ['None', '']:
94 --flye_assembly_info_file '$flye_assembly_info_file' 94 --flye_assembly_info_file '$flye_assembly_info_file'
95 --flye_version '$flye_version' 95 --flye_version '$flye_version'
96 #end if 96 #end if
97 --genome_insertions_file '$genome_insertions_file' 97 --genome_insertions_file '$genome_insertions_file'
98 #if $illumina_fastq_file.ext.endswith(".gz"): 98 #if $ont_fastq_file.ext.endswith(".gz"):
99 --gzipped 99 --gzipped
100 #end if 100 #end if
101 --illumina_fastq_file '$illumina_fastq_file' 101 --ont_fastq_file '$ont_fastq_file'
102 #if str($kraken2_report_file) not in ['None', '']: 102 #if str($kraken2_report_file) not in ['None', '']:
103 --kraken2_report_file '$kraken2_report_file' 103 --kraken2_report_file '$kraken2_report_file'
104 --kraken2_version '$kraken2_version' 104 --kraken2_version '$kraken2_version'
105 #end if 105 #end if
106 #if str($minimap2_bam_file) not in ['None', '']: 106 #if str($minimap2_bam_file) not in ['None', '']:
134 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 134 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
135 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 135 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
136 <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"/> 136 <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"/>
137 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 137 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
138 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> 138 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
139 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 139 <param name="ont_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT fastq sample file"/>
140 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> 140 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
141 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 141 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
142 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 142 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
143 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> 143 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
144 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> 144 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
152 <tests> 152 <tests>
153 <test> 153 <test>
154 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/> 154 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
155 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/> 155 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
156 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/> 156 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
157 <param name="illumina_fastq_file" value="illumina_fastq.fastq" ftype="fastq"/> 157 <param name="ont_fastq_file" value="ont_fastq.fastq" ftype="fastq"/>
158 <output name="output" value="output.pdf" ftype="pdf"/> 158 <output name="output" value="output.pdf" ftype="pdf"/>
159 </test> 159 </test>
160 </tests> 160 </tests>
161 <help> 161 <help>
162 **What it does** 162 **What it does**