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comparison pima_report.xml @ 13:f03c80bb22e9 draft

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Uploaded
author greg
date Thu, 16 Mar 2023 14:42:13 +0000
parents 99613333fd1f
children 95b1d1a9497d
comparison
equal deleted inserted replaced
12:99613333fd1f 13:f03c80bb22e9
34 #if str($varscan_vcf_file) not in ['None', '']: 34 #if str($varscan_vcf_file) not in ['None', '']:
35 #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier)) 35 #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
36 #end if 36 #end if
37 37
38 mkdir amr_matrix_png_dir && 38 mkdir amr_matrix_png_dir &&
39 mkdir circos_png_dir &&
39 mkdir feature_bed_dir && 40 mkdir feature_bed_dir &&
40 mkdir feature_png_dir && 41 mkdir feature_png_dir &&
41 mkdir mutation_regions_dir && 42 mkdir mutation_regions_dir &&
42 touch 'pima_report.pdf' && 43 touch 'pima_report.pdf' &&
43 44
44 #for $i in $amr_matrices_png: 45 #for $i in $amr_matrices_png:
45 #set file_name = $i.file_name 46 #set file_name = $i.file_name
46 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 47 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
47 ln -s $i 'amr_matrix_png_dir/$identifier' && 48 ln -s $i 'amr_matrix_png_dir/$identifier' &&
49 #end for
50 #for $i in $circos_png:
51 #set file_name = $i.file_name
52 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
53 ln -s $i 'circos_png_dir/$identifier' &&
48 #end for 54 #end for
49 #for $i in $features_bed: 55 #for $i in $features_bed:
50 #set file_name = $i.file_name 56 #set file_name = $i.file_name
51 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 57 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
52 ln -s $i 'feature_bed_dir/$identifier' && 58 ln -s $i 'feature_bed_dir/$identifier' &&
72 --bedtools_version '$bedtools_version' 78 --bedtools_version '$bedtools_version'
73 #end if 79 #end if
74 #if str($blastn_features) not in ['None', '']: 80 #if str($blastn_features) not in ['None', '']:
75 --blastn_version '$blastn_version' 81 --blastn_version '$blastn_version'
76 #end if 82 #end if
83 --circos_png_dir 'circos_png_dir'
77 --compute_sequence_length_file '$compute_sequence_length_file' 84 --compute_sequence_length_file '$compute_sequence_length_file'
78 --contig_coverage_file '$contig_coverage_file' 85 --contig_coverage_file '$contig_coverage_file'
79 --dbkey '$aligned_sample.metadata.dbkey' 86 --dbkey '$aligned_sample.metadata.dbkey'
80 --dnadiff_snps_file '$dnadiff_snps_file' 87 --dnadiff_snps_file '$dnadiff_snps_file'
81 #if str($dnadiff_snps_file) not in ['None', '']: 88 #if str($dnadiff_snps_file) not in ['None', '']:
101 #end if 108 #end if
102 --mutation_regions_dir 'mutation_regions_dir' 109 --mutation_regions_dir 'mutation_regions_dir'
103 --mutation_regions_bed_file '$mutation_regions_bed_file' 110 --mutation_regions_bed_file '$mutation_regions_bed_file'
104 --pima_css '${__tool_directory__}/pima.css' 111 --pima_css '${__tool_directory__}/pima.css'
105 --plasmids_file '$plasmids_file' 112 --plasmids_file '$plasmids_file'
113 --quast_report_file '$quast_report_file'
106 --reference_insertions_file '$reference_insertions_file' 114 --reference_insertions_file '$reference_insertions_file'
107 #if str($samtools_pileup_file) not in ['None', '']: 115 #if str($samtools_pileup_file) not in ['None', '']:
108 --samtools_version '$samtools_version' 116 --samtools_version '$samtools_version'
109 #end if 117 #end if
110 #if str($varscan_vcf_file) not in ['None', '']: 118 #if str($varscan_vcf_file) not in ['None', '']:
117 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/> 125 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
118 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/> 126 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
119 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/> 127 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
120 <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/> 128 <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
121 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/> 129 <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"/>
122 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 131 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
123 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 132 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
124 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 133 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
125 <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"/>
126 <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"/>
129 <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"/>
130 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 139 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
131 <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"/>
132 <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"/>
133 <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"/>
134 <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"/>
135 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/> 145 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
136 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/> 146 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
137 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/> 147 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
138 </inputs> 148 </inputs>