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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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10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
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11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
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2
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12
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5
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13 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
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14 #set blastn_version = $blastn_version.rstrip('(features)')
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2
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15 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
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16 #set dnadiff_version = $dnadiff_version.rstrip('(snps)')
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1
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17 #if str($flye_assembly_info_file) not in ['None', '']:
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18 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
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19 #set flye_version = $flye_version.rstrip('(assembly info)')
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20 #end if
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2
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21 #if str($kraken2_report_file) not in ['None', '']:
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22 #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
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23 #set kraken2_version = $kraken2_version.rstrip('(report)')
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24 #end if
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0
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25
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1
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26 mkdir amr_matrix_png_dir &&
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27 mkdir feature_bed_dir &&
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28 mkdir feature_png_dir &&
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29 mkdir mutation_regions_dir &&
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30 touch 'pima_report.pdf' &&
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31
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1
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32 #for $i in $amr_matrices_png:
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33 #set file_name = $i.file_name
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34 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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35 ln -s $i 'amr_matrix_png_dir/$identifier' &&
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36 #end for
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37 #for $i in $features_bed:
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38 #set file_name = $i.file_name
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39 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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40 ln -s $i 'feature_bed_dir/$identifier' &&
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41 #end for
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42 #for $i in $features_png:
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43 #set file_name = $i.file_name
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44 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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45 ln -s $i 'feature_png_dir/$identifier' &&
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46 #end for
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47 #for $i in $mutation_regions:
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48 #set file_name = $i.file_name
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49 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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50 ln -s $i 'mutation_regions_dir/$identifier' &&
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51 #end for
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52
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53 python '${__tool_directory__}/pima_report.py'
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1
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54 --amr_matrix_png_dir 'amr_matrix_png_dir'
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55 --amr_deletions_file '$amr_deletions_file'
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56 --analysis_name '$analysis_name'
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57 --assembly_fasta_file '$assembly_fasta_file'
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58 --assembly_name '$assembly_name'
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5
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59 --blastn_version '$blastn_version'
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60 --compute_sequence_length_file '$compute_sequence_length_file'
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61 --contig_coverage_file '$contig_coverage_file'
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62 --dbkey '$aligned_sample.metadata.dbkey'
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63 --dnadiff_snps_file '$dnadiff_snps_file'
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2
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64 --dnadiff_version '$dnadiff_version'
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65 --feature_bed_dir 'feature_bed_dir'
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66 --feature_png_dir 'feature_png_dir'
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1
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67 #if str($flye_assembly_info_file) not in ['None', '']:
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68 --flye_assembly_info_file '$flye_assembly_info_file'
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69 --flye_version '$flye_version'
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70 #end if
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71 --genome_insertions_file '$genome_insertions_file'
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72 #if $illumina_fastq_file.ext.endswith(".gz"):
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73 --gzipped
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74 #end if
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75 --illumina_fastq_file '$illumina_fastq_file'
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2
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76 #if str($kraken2_report_file) not in ['None', '']:
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77 --kraken2_report_file '$kraken2_report_file'
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78 --kraken2_version '$kraken2_version'
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79 #end if
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80 --mutation_regions_dir 'mutation_regions_dir'
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81 --mutation_regions_bed_file '$mutation_regions_bed_file'
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82 --pima_css '${__tool_directory__}/pima.css'
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83 --plasmids_file '$plasmids_file'
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84 --reference_insertions_file '$reference_insertions_file'
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85 && mv 'pima_report.pdf' '$output'
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86 ]]></command>
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87 <inputs>
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88 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
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89 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
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1
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90 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
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91 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
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4
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92 <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
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1
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93 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
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94 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
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95 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
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96 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
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97 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
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98 <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"/>
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99 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
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100 <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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101 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
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102 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
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103 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
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104 <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
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105 <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
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106 </inputs>
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107 <outputs>
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108 <data name="output" format="pdf"/>
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109 </outputs>
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110 <tests>
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111 <test>
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112 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
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113 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
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114 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
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115 <param name="illumina_fastq_file" value="illumina_fastq.fastq" ftype="fastq"/>
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116 <output name="output" value="output.pdf" ftype="pdf"/>
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117 </test>
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118 </tests>
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119 <help>
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120 **What it does**
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121
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122 Generates the PIMA analysis summary report.
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123 </help>
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124 <expand macro="citations"/>
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125 </tool>
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126
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