Mercurial > repos > greg > pima_report

comparison pima_report.xml @ 18:e948214a9e3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 22 Mar 2023 13:07:22 +0000
parents 95b1d1a9497d
children 667b253329c6
comparison
equal deleted inserted replaced
17:b4ed9f55de13 18:e948214a9e3c
86 --dbkey '$aligned_sample.metadata.dbkey' 86 --dbkey '$aligned_sample.metadata.dbkey'
87 --dnadiff_snps_file '$dnadiff_snps_file' 87 --dnadiff_snps_file '$dnadiff_snps_file'
88 #if str($dnadiff_snps_file) not in ['None', '']: 88 #if str($dnadiff_snps_file) not in ['None', '']:
89 --dnadiff_version '$dnadiff_version' 89 --dnadiff_version '$dnadiff_version'
90 #end if 90 #end if
91 --errors_file '$errors_file'
91 --feature_bed_dir 'feature_bed_dir' 92 --feature_bed_dir 'feature_bed_dir'
92 --feature_png_dir 'feature_png_dir' 93 --feature_png_dir 'feature_png_dir'
93 #if str($flye_assembly_info_file) not in ['None', '']: 94 #if str($flye_assembly_info_file) not in ['None', '']:
94 --flye_assembly_info_file '$flye_assembly_info_file' 95 --flye_assembly_info_file '$flye_assembly_info_file'
95 --flye_version '$flye_version' 96 --flye_version '$flye_version'
109 --mutation_regions_dir 'mutation_regions_dir' 110 --mutation_regions_dir 'mutation_regions_dir'
110 --mutation_regions_bed_file '$mutation_regions_bed_file' 111 --mutation_regions_bed_file '$mutation_regions_bed_file'
111 --pima_css '${__tool_directory__}/pima.css' 112 --pima_css '${__tool_directory__}/pima.css'
112 --plasmids_file '$plasmids_file' 113 --plasmids_file '$plasmids_file'
113 --quast_report_file '$quast_report_file' 114 --quast_report_file '$quast_report_file'
115 --read_type '$read_type'
114 --reference_insertions_file '$reference_insertions_file' 116 --reference_insertions_file '$reference_insertions_file'
115 #if str($samtools_pileup_file) not in ['None', '']: 117 #if str($samtools_pileup_file) not in ['None', '']:
116 --samtools_version '$samtools_version' 118 --samtools_version '$samtools_version'
117 #end if 119 #end if
118 #if str($varscan_vcf_file) not in ['None', '']: 120 #if str($varscan_vcf_file) not in ['None', '']:
129 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/> 131 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
130 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/> 132 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
131 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 133 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
132 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 134 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
133 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 135 <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"/>
134 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 137 <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"/> 138 <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"/> 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"/>
137 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 140 <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"/> 141 <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="ont_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT fastq sample file"/> 142 <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"/> 143 <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"/> 144 <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"/> 145 <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"/> 146 <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">
148 <option value="ont" selected="true">Long reads - Oxford Nanopore Technologies (ONT)</option>
149 <option value="illumina">Short reads - Illumina</option>
150 </param>
144 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/> 151 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
145 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> 152 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
146 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> 153 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
147 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/> 154 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
148 </inputs> 155 </inputs>