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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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26
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10 #if str($read_type_cond.read_type) == 'ont':
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11 #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.ont_file.element_identifier))
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25
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12 #else:
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26
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13 #set analysis_name = re.sub('[^\s\w\-]', '_', str($read_type_cond.illumina_forward_read.element_identifier))
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25
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14 #end if
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0
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15 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
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2
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16
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12
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17 #if str($bedtools_complementbed_file) not in ['None', '']:
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18 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
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19 #end if
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20 #if str($blastn_features) not in ['None', '']:
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21 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
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22 #end if
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23 #if str($dnadiff_snps_file) not in ['None', '']:
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24 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
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25 #end if
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26
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26
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27 ## All ONT samples are single-end reads, while all Illumina samples are
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28 ## sets if paired reads. For ONT, we need both an assembly_fasta_file
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29 ## which is produced by the medaka pipeline and and assembler_version_file
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30 ## which is produced by flye. For Illumina we need only the assembly_fasta_file
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31 ## which is produced by SPAdes since the version can be derived from it.
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32 #if str($assembler_version_file) in ['None', '']:
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33 ## We're analyzing a set of Illumina paired reads.
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34 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
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35 #else:
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36 ## We're analyzing an ONT sample.
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21
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37 #set assembler_version = re.sub('[^\s\w\-]', '_', str($assembler_version_file.element_identifier))
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1
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38 #end if
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26
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39
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2
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40 #if str($kraken2_report_file) not in ['None', '']:
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41 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
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12
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42 #end if
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43 #if str($minimap2_bam_file) not in ['None', '']:
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44 #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
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45 #end if
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46 #if str($samtools_pileup_file) not in ['None', '']:
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47 #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier))
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48 #end if
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49 #if str($varscan_vcf_file) not in ['None', '']:
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50 #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
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2
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51 #end if
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0
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52
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1
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53 mkdir amr_matrix_png_dir &&
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13
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54 mkdir circos_png_dir &&
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55 mkdir feature_bed_dir &&
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56 mkdir feature_png_dir &&
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57 mkdir mutation_regions_dir &&
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58 touch 'pima_report.pdf' &&
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59
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1
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60 #for $i in $amr_matrices_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 $i 'amr_matrix_png_dir/$identifier' &&
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64 #end for
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13
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65 #for $i in $circos_png:
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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 $i 'circos_png_dir/$identifier' &&
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69 #end for
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0
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70 #for $i in $features_bed:
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71 #set file_name = $i.file_name
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72 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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73 ln -s $i 'feature_bed_dir/$identifier' &&
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74 #end for
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75 #for $i in $features_png:
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76 #set file_name = $i.file_name
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77 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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78 ln -s $i 'feature_png_dir/$identifier' &&
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79 #end for
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80 #for $i in $mutation_regions:
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81 #set file_name = $i.file_name
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82 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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83 ln -s $i 'mutation_regions_dir/$identifier' &&
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84 #end for
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85
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29
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86 #if str($lrn_risk_amr_files) != 'None':
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87 touch 'lrn_risk_amr.tsv' &&
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88 #for $i in $lrn_risk_amr_files:
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89 cat $i >> 'lrn_risk_amr.tsv' &&
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28
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90 #end for
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91 #end if
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92
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29
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93 #if str($lrn_risk_blacklist_files) != 'None':
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94 touch 'lrn_risk_blacklist.tsv' &&
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95 #for $i in $lrn_risk_blacklist_files:
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96 cat $i >> 'lrn_risk_blacklist.tsv' &&
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28
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97 #end for
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98 #end if
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99
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29
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100 #if str($lrn_risk_vf_files) != 'None':
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101 touch 'lrn_risk_vf.tsv' &&
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102 #for $i in $lrn_risk_vf_files:
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103 cat $i >> 'lrn_risk_vf.tsv' &&
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28
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104 #end for
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105 #end if
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106
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107 python '${__tool_directory__}/pima_report.py'
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108 --amr_matrix_png_dir 'amr_matrix_png_dir'
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109 --amr_deletions_file '$amr_deletions_file'
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110 --analysis_name '$analysis_name'
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111 --assembly_fasta_file '$assembly_fasta_file'
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112 --assembly_name '$assembly_name'
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12
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113 #if str($bedtools_complementbed_file) not in ['None', '']:
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114 --bedtools_version '$bedtools_version'
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115 #end if
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116 #if str($blastn_features) not in ['None', '']:
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117 --blastn_version '$blastn_version'
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118 #end if
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119 --circos_png_dir 'circos_png_dir'
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1
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120 --compute_sequence_length_file '$compute_sequence_length_file'
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121 --contig_coverage_file '$contig_coverage_file'
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122 --dbkey '$aligned_sample.metadata.dbkey'
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1
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123 --dnadiff_snps_file '$dnadiff_snps_file'
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12
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124 #if str($dnadiff_snps_file) not in ['None', '']:
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125 --dnadiff_version '$dnadiff_version'
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126 #end if
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127 --errors_file '$errors_file'
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128 --feature_bed_dir 'feature_bed_dir'
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129 --feature_png_dir 'feature_png_dir'
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21
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130 #if str($assembler_version_file) not in ['None', '']:
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131 --assembler_version '$assembler_version'
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26
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132 #if str($read_type_cond.read_type) == 'ont':
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21
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133 ## Need to pass the tabular flye assembly file.
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134 --flye_assembly_info_file '$assembler_version_file'
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135 #end if
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1
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136 #end if
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137 --genome_insertions_file '$genome_insertions_file'
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138 #if str($read_type_cond.read_type) == 'ont':
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139 ## We're analyzing a single-edn ONT sample.
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140 #if $read_type_cond.ont_file.ext.endswith(".gz"):
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141 --gzipped
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142 #end if
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143 --ont_file '$read_type_cond.ont_file'
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144 #else:
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145 ## We're analyzing a set of Illumina paired reads.
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146 #if $read_type_cond.illumina_forward_read.ext.endswith(".gz"):
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147 --gzipped
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148 #end if
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149 --illumina_forward_read_file '$read_type_cond.illumina_forward_read'
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150 --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read'
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151 #end if
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2
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152 #if str($kraken2_report_file) not in ['None', '']:
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153 --kraken2_report_file '$kraken2_report_file'
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154 --kraken2_version '$kraken2_version'
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155 #end if
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29
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156 --lrn_risk_amr_file 'lrn_risk_amr.tsv'
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157 --lrn_risk_blacklist_file 'lrn_risk_blacklist.tsv'
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158 --lrn_risk_vf_file 'lrn_risk_vf.tsv'
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159 #if str($minimap2_bam_file) not in ['None', '']:
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160 --minimap2_version '$minimap2_version'
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161 #end if
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162 --mutation_regions_dir 'mutation_regions_dir'
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163 --mutation_regions_bed_file '$mutation_regions_bed_file'
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164 --pima_css '${__tool_directory__}/pima.css'
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165 --plasmids_file '$plasmids_file'
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166 --quast_report_file '$quast_report_file'
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167 --read_type '$read_type_cond.read_type'
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168 --reference_insertions_file '$reference_insertions_file'
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169 #if str($samtools_pileup_file) not in ['None', '']:
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170 --samtools_version '$samtools_version'
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171 #end if
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172 #if str($varscan_vcf_file) not in ['None', '']:
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173 --varscan_version '$varscan_version'
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174 #end if
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175 && mv 'pima_report.pdf' '$output'
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176 ]]></command>
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177 <inputs>
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178 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
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179 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
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180 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
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181 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
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182 <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
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183 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
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184 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
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185 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
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186 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
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187 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
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188 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
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189 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
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190 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
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191 <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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192 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
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193 <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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194 <param name="lrn_risk_amr_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk AMR files"/>
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195 <param name="lrn_risk_blacklist_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk blacklist files"/>
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196 <param name="lrn_risk_vf_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk virulence factors files"/>
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197 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
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198 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
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199 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
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200 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
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201 <conditional name="read_type_cond">
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202 <param argument="--read_type" type="select" label="Specify the read type">
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203 <option value="ont" selected="true">ONT single read</option>
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204 <option value="illumina">Illumina read pair</option>
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205 </param>
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206 <when value="ont">
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207 <param name="ont_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT single read sample file"/>
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208 </when>
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209 <when value="illumina">
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210 <param name="illumina_forward_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina forward read sample file"/>
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211 <param name="illumina_reverse_read" format="fastqsanger,fastqsanger.gz" type="data" label="Illumina reverse read sample file"/>
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212 </when>
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213 </conditional>
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214 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
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23
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215 <param name="plasmids_file" type="data" format="tsv" optional="true" label="pChunks plasmids TSV file" help="Optional, ignored if not selected"/>
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216 <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
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217 <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
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218 </inputs>
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219 <outputs>
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220 <data name="output" format="pdf"/>
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221 </outputs>
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222 <tests>
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223 <test>
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224 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
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225 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
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226 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
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227 <param name="read_type" value="ont"/>
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228 <param name="ont_file" value="ont_fastq.fastq" ftype="fastq"/>
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229 <output name="output" value="output.pdf" ftype="pdf"/>
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230 </test>
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231 </tests>
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232 <help>
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233 **What it does**
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234
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235 Generates the PIMA analysis summary report.
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236 </help>
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237 <expand macro="citations"/>
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238 </tool>
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239
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