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1 <tool id="pima_report" name="PIMA: summary report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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21
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10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
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0
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11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
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2
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12
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12
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13 #if str($bedtools_complementbed_file) not in ['None', '']:
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14 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
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15 #end if
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16 #if str($blastn_features) not in ['None', '']:
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17 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
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18 #end if
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19 #if str($dnadiff_snps_file) not in ['None', '']:
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20 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
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21 #end if
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21
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22 #if str($assembler_version_file) not in ['None', '']:
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23 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier))
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1
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24 #end if
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2
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25 #if str($kraken2_report_file) not in ['None', '']:
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26 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
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12
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27 #end if
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28 #if str($minimap2_bam_file) not in ['None', '']:
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29 #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
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30 #end if
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31 #if str($samtools_pileup_file) not in ['None', '']:
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32 #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier))
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33 #end if
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34 #if str($varscan_vcf_file) not in ['None', '']:
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35 #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
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2
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36 #end if
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0
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37
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1
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38 mkdir amr_matrix_png_dir &&
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13
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39 mkdir circos_png_dir &&
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0
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40 mkdir feature_bed_dir &&
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41 mkdir feature_png_dir &&
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42 mkdir mutation_regions_dir &&
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43 touch 'pima_report.pdf' &&
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44
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1
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45 #for $i in $amr_matrices_png:
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46 #set file_name = $i.file_name
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47 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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48 ln -s $i 'amr_matrix_png_dir/$identifier' &&
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49 #end for
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13
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50 #for $i in $circos_png:
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51 #set file_name = $i.file_name
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52 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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53 ln -s $i 'circos_png_dir/$identifier' &&
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54 #end for
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0
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55 #for $i in $features_bed:
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56 #set file_name = $i.file_name
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57 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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58 ln -s $i 'feature_bed_dir/$identifier' &&
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59 #end for
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60 #for $i in $features_png:
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61 #set file_name = $i.file_name
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62 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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63 ln -s $i 'feature_png_dir/$identifier' &&
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64 #end for
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65 #for $i in $mutation_regions:
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66 #set file_name = $i.file_name
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67 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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68 ln -s $i 'mutation_regions_dir/$identifier' &&
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69 #end for
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70
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71 python '${__tool_directory__}/pima_report.py'
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1
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72 --amr_matrix_png_dir 'amr_matrix_png_dir'
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73 --amr_deletions_file '$amr_deletions_file'
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74 --analysis_name '$analysis_name'
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75 --assembly_fasta_file '$assembly_fasta_file'
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76 --assembly_name '$assembly_name'
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12
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77 #if str($bedtools_complementbed_file) not in ['None', '']:
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78 --bedtools_version '$bedtools_version'
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79 #end if
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80 #if str($blastn_features) not in ['None', '']:
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81 --blastn_version '$blastn_version'
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82 #end if
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13
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83 --circos_png_dir 'circos_png_dir'
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1
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84 --compute_sequence_length_file '$compute_sequence_length_file'
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85 --contig_coverage_file '$contig_coverage_file'
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86 --dbkey '$aligned_sample.metadata.dbkey'
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1
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87 --dnadiff_snps_file '$dnadiff_snps_file'
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12
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88 #if str($dnadiff_snps_file) not in ['None', '']:
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89 --dnadiff_version '$dnadiff_version'
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90 #end if
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18
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91 --errors_file '$errors_file'
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0
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92 --feature_bed_dir 'feature_bed_dir'
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93 --feature_png_dir 'feature_png_dir'
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21
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94 #if str($assembler_version_file) not in ['None', '']:
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95 --assembler_version '$assembler_version'
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96 #if str($read_type) == 'ont':
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97 ## Need to pass the tabular flye assembly file.
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98 --flye_assembly_info_file '$assembler_version_file'
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99 #end if
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1
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100 #end if
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101 --genome_insertions_file '$genome_insertions_file'
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21
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102 #if $fastq_file.ext.endswith(".gz"):
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0
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103 --gzipped
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104 #end if
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21
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105 --fastq_file '$fastq_file'
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2
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106 #if str($kraken2_report_file) not in ['None', '']:
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107 --kraken2_report_file '$kraken2_report_file'
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108 --kraken2_version '$kraken2_version'
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109 #end if
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12
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110 #if str($minimap2_bam_file) not in ['None', '']:
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111 --minimap2_version '$minimap2_version'
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112 #end if
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113 --mutation_regions_dir 'mutation_regions_dir'
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114 --mutation_regions_bed_file '$mutation_regions_bed_file'
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115 --pima_css '${__tool_directory__}/pima.css'
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116 --plasmids_file '$plasmids_file'
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117 --quast_report_file '$quast_report_file'
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18
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118 --read_type '$read_type'
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119 --reference_insertions_file '$reference_insertions_file'
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12
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120 #if str($samtools_pileup_file) not in ['None', '']:
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121 --samtools_version '$samtools_version'
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122 #end if
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123 #if str($varscan_vcf_file) not in ['None', '']:
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124 --varscan_version '$varscan_version'
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125 #end if
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126 && mv 'pima_report.pdf' '$output'
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127 ]]></command>
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128 <inputs>
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1
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129 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
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0
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130 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
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1
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131 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
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0
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132 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
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12
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133 <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
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4
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134 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
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13
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135 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
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1
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136 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
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137 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
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138 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
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139 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
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21
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140 <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
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141 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
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142 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
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21
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143 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
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144 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
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2
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145 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
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146 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
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147 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
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148 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
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149 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
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150 <param argument="--read_type" type="select" label="Specify the read type">
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151 <option value="ont" selected="true">Long reads - Oxford Nanopore Technologies (ONT)</option>
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152 <option value="illumina">Short reads - Illumina</option>
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153 </param>
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154 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
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155 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
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156 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
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157 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
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158 </inputs>
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159 <outputs>
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160 <data name="output" format="pdf"/>
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161 </outputs>
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162 <tests>
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163 <test>
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164 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
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165 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
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166 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
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167 <param name="fastq_file" value="ont_fastq.fastq" ftype="fastq"/>
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168 <output name="output" value="output.pdf" ftype="pdf"/>
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169 </test>
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170 </tests>
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171 <help>
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172 **What it does**
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173
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174 Generates the PIMA analysis summary report.
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175 </help>
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176 <expand macro="citations"/>
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177 </tool>
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178
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