Mercurial > repos > pimarin > abromics_galaxy_json_extractor

annotate abromics_galaxy_json_extractor.xml @ 0:c49ec8c0b046 draft

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author pimarin
date Sun, 04 Jun 2023 17:16:20 +0000
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children 421032d8dd5d
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1 <tool id="abromics_galaxy_json_extractor" name="abromics_galaxy_json_extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Result extractor to json format
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4 </description>
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5 <macros>
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6 <import>macro.xml</import>
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7 </macros>
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8 <expand macro='edam'/>
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9 <expand macro="requirements"/>
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10 <expand macro="version_command"/>
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11
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12 <command detect_errors="aggressive"><![CDATA[
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13 mkdir "abromics_extracted_folder" &&
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14 #*=================================================================
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15 Paramaters to add Database and tool version if available
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16 =================================================================*#
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17 #set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
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18 #set $counter = len($tool_section.tools)-1
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19 #*======================================================
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20 Loop to include some different tool in one time
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21 ======================================================*#
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22 #for $i, $tool in enumerate( $tool_section.tools )
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23 abromics_extract
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24 "$tool.select_tool.tool_list"
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25 --hid $tool.select_tool.input.hid
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26 "$tool.select_tool.input"
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27 --analysis_software_version "$tool.select_tool.analysis_software_version"
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28 #if str($tool.select_tool.tool_list) in str($software_with_database)
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29 --reference_database_version "$tool.select_tool.reference_database_version"
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30 #end if
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31 #if "$tool.select_tool.tool_list" == "bakta"
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32 --summary_result_path "$tool.select_tool.summary_result_path"
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33 --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
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34 --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
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35 --gff_file_path "$tool.select_tool.gff_file_path"
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36 #elif "$tool.select_tool.tool_list" == "bracken"
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37 --kraken_report_path "tool.select_tool.kraken_report_path"
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38 --threshold "tool.select_tool.threshold"
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39 --read_length "tool.select_tool.read_length"
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40 --level "tool.select_tool.level"
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41 #elif"$tool.select_tool.tool_list" == "integronfinder2"
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42 --summary_file_path "tool.select_tool.summary_file_path"
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43 #elif "$tool.select_tool.tool_list" == "isescan"
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44 --orf_fna_file "tool.select_tool.orf_fna_file"
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45 --orf_faa_file "tool.select_tool.orf_faa_file"
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46 --is_fna_file "tool.select_tool.is_fna_file"
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47 #elif "$tool.select_tool.tool_list" == "kraken2"
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48 --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
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49 #elif "$tool.select_tool.tool_list" == "plasmidfinder"
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50 --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
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51 --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
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52 #elif "$tool.select_tool.tool_list" == "recentrifuge"
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53 --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
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54 --rcf_html_path "tool.select_tool.rcf_html_path"
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55 #elif "$tool.select_tool.tool_list" == "shovill"
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56 --contig_graph_path "tool.select_tool.contig_graph_path"
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57 --bam_file_path "tool.select_tool.bam_file_path"
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58 #elif "$tool.select_tool.tool_list" == "staramr"
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59 --mlst_file_path "tool.select_tool.mlst_file_path"
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60 --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
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61 --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
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62 --setting_file_path "tool.select_tool.setting_file_path"
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63 #elif "$tool.select_tool.tool_list" == "tabular_file"
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64 --analysis_software_name "tool.select_tool.analysis_software_name"
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65 #end if
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66 -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
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67 | tee "$logfile"
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68 #if $i < $counter
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69 &&
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70 #end if
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71 #end for
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72
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73 ]]>
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74 </command>
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75 <inputs>
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76 <section name="tool_section" title="Available tools" expanded="true">
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77 <repeat name="tools" title="Tool" min="0">
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78 <conditional name="select_tool">
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79 <param name="tool_list" type="select" label="Available tools">
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80 <option value="abricate">abricate</option>
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81 <option value="bakta">bakta</option>
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82 <option value="bandage">bandage</option>
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83 <option value="bracken">bracken</option>
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84 <option value="fastp">fastp</option>
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85 <option value="integronfinder2">integronfinder2</option>
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86 <option value="isescan">isescan</option>
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87 <option value="kraken2">kraken2</option>
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88 <option value="plasmidfinder">plasmidfinder</option>
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89 <option value="quast">quast</option>
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90 <option value="recentrifuge">recentrifuge</option>
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91 <option value="refseqmasher">refseqmasher</option>
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92 <option value="shovill">shovill</option>
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93 <option value="staramr">staramr</option>
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94 <option value="tabular_file">tabular_generic_file</option>
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95 </param>
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96 <when value="abricate">
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97 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
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98 <expand macro="analysis_software_version"/>
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99 <expand macro="reference_database_version"/>
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100 </when>
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101 <when value="bakta">
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102 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
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103 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
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104 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide file" help="Nucleotide sequence annotation file"/>
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105 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
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106 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
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107 <expand macro="analysis_software_version"/>
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108 <expand macro="reference_database_version"/>
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109 </when>
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110 <when value="bandage">
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111 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
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112 <expand macro="analysis_software_version"/>
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113 </when>
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114 <when value="bracken">
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115 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
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116 <expand macro="analysis_software_version"/>
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117 <expand macro="reference_database_version"/>
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118 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
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119 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
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120 <param argument="--read_length" type="integer" min="0" optional="true" label="Read length"/>
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121 <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
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122 <option value="D">Domain</option>
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123 <option value="P">Phylum</option>
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124 <option value="C">Class</option>
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125 <option value="O">Order</option>
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126 <option value="F">Family</option>
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127 <option value="G">Genus</option>
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128 <option value="S">Species</option>
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129 <option value="S+">Subspecies</option>
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130 </param>
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131 </when>
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132 <when value="fastp">
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133 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
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134 <expand macro="analysis_software_version"/>
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135 </when>
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136 <when value="integronfinder2">
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137 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
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138 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
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139 <expand macro="analysis_software_version"/>
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140 </when>
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141 <when value="isescan">
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142 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
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143 <param argument="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
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144 <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
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145 <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
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146 <expand macro="analysis_software_version"/>
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147 </when>
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148 <when value="kraken2">
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149 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
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150 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
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151 <expand macro="analysis_software_version"/>
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152 <expand macro="reference_database_version"/>
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153 </when>
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154 <when value="plasmidfinder">
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155 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
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156 <param argument="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
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157 <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
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158 <expand macro="analysis_software_version"/>
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159 <expand macro="reference_database_version"/>
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160 </when>
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161 <when value="quast">
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162 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
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163 <expand macro="analysis_software_version"/>
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164 </when>
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165 <when value="recentrifuge">
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166 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
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167 <param argument="--rcf_stat_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
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168 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
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169 <expand macro="analysis_software_version"/>
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170 <expand macro="reference_database_version"/>
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171 </when>
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172 <when value="refseqmasher">
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173 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
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174 <expand macro="analysis_software_version"/>
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175 </when>
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176 <when value="shovill">
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177 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
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178 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
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179 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
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180 <expand macro="analysis_software_version"/>
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181
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182 </when>
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183 <when value="staramr">
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184 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
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185 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
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186 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
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187 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
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188 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
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189 <expand macro="analysis_software_version"/>
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190 </when>
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191 <when value="tabular_file">
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192 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
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193 <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
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194 <expand macro="analysis_software_version"/>
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195 </when>
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196 </conditional>
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197 </repeat>
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198 </section>
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199 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
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200 </inputs>
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201 <outputs>
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202 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
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203 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
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204 </collection>
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205 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
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206 <filter> log == True </filter>
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207 </data>
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208 </outputs>
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209 <tests>
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210 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
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211 <section name="tool_section">
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212 <repeat name="tools">
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213 <conditional name="select_tool">
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214 <param name="tool_list" value="abricate"/>
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215 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
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216 <param name="analysis_software_version" value="1.0"/>
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217 <param name="reference_database_version" value="2.0" />
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218 </conditional>
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219 </repeat>
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220 </section>
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221 <param name="log" value="true"/>
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222 <output_collection name="output_json" type="list">
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223 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
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224 </output_collection>
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225 <output name="logfile" value="abricate_logfile.txt"/>
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226 </test>
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227 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
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228 <section name="tool_section">
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229 <repeat name="tools">
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230 <conditional name="select_tool">
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231 <param name="tool_list" value="bakta"/>
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232 <param name="input" value="bakta/bakta.json" ftype="json"/>
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233 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
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234 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide.fasta" ftype="fasta"/>
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235 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
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236 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
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237 <param name="reference_database_version" value="1.6.1"/>
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238 </conditional>
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239 </repeat>
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240 </section>
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241 <output_collection name="output_json" type="list" count="1">
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242 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
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243 </output_collection>
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244 </test>
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245 <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
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246 <section name="tool_section">
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247 <repeat name="tools">
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248 <conditional name="select_tool">
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249 <param name="tool_list" value="abricate"/>
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250 <param name="input" value="abricate/report.tsv" ftype="tabular"/>
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251 <param name="analysis_software_version" value="1.0"/>
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252 <param name="reference_database_version" value="2.0" />
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253 </conditional>
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254 </repeat>
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255 <repeat name="tools">
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256 <conditional name="select_tool">
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257 <param name="tool_list" value="bakta"/>
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258 <param name="input" value="bakta/bakta.json" ftype="json"/>
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259 </conditional>
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260 </repeat>
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261 <repeat name="tools">
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262 <conditional name="select_tool">
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263 <param name="tool_list" value="bandage"/>
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264 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
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265 </conditional>
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266 </repeat>
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267 <repeat name="tools">
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268 <conditional name="select_tool">
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269 <param name="tool_list" value="bracken"/>
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270 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
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271 <param name="bracken/bracken_kraken_report" ftype="tabular" />
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272 <param name="threshold" value="0" />
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273 <param name="read_length" value="100"/>
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274 <param name="level" value="S"/>
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275 </conditional>
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276 </repeat>
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277 <repeat name="tools">
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278 <conditional name="select_tool">
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279 <param name="tool_list" value="fastp"/>
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280 <param name="input" value="fastp/fastp_report.json" ftype="json"/>
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281 </conditional>
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282 </repeat>
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283 <repeat name="tools">
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284 <conditional name="select_tool">
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285 <param name="tool_list" value="integronfinder2"/>
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286 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
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287 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
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288 </conditional>
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289 </repeat>
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290 <repeat name="tools">
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291 <conditional name="select_tool">
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292 <param name="tool_list" value="isescan"/>
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293 <param name="input" value="isescan/results.tsv" ftype="tabular"/>
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294 <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
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295 <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
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296 <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
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297 </conditional>
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298 </repeat>
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299 <repeat name="tools">
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300 <conditional name="select_tool">
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301 <param name="tool_list" value="kraken2"/>
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302 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
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303 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
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304 </conditional>
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305 </repeat>
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306 <repeat name="tools">
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307 <conditional name="select_tool">
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308 <param name="tool_list" value="plasmidfinder"/>
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309 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
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310 <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
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311 <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
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312 </conditional>
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313 </repeat>
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314 <repeat name="tools">
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315 <conditional name="select_tool">
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316 <param name="tool_list" value="quast"/>
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317 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
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318 </conditional>
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319 </repeat>
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320 <repeat name="tools">
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321 <conditional name="select_tool">
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322 <param name="tool_list" value="recentrifuge"/>
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323 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
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324 <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
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325 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
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326 </conditional>
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327 </repeat>
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328 <repeat name="tools">
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329 <conditional name="select_tool">
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330 <param name="tool_list" value="refseqmasher"/>
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331 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
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332 </conditional>
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333 </repeat>
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334 <repeat name="tools">
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335 <conditional name="select_tool">
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336 <param name="tool_list" value="shovill"/>
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337 <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
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338 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
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339 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
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340 </conditional>
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341 </repeat>
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342 <repeat name="tools">
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343 <conditional name="select_tool">
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344 <param name="tool_list" value="staramr"/>
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345 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
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346 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
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347 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
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348 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
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349 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
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350 </conditional>
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351 </repeat>
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352 <repeat name="tools">
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353 <conditional name="select_tool">
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354 <param name="tool_list" value="tabular_file"/>
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355 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
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356 </conditional>
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357 </repeat>
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358 </section>
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359 <output_collection name="output_json" type="list" count="15">
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360 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
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361 <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
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362 <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
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363 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
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364 <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
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365 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
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366 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
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367 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
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368 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
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369 <expand macro="element_assert" name="quast_9_output" text="2944723"/>
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370 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
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371 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
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372 <expand macro="element_assert" name="shovill_12_output" text="436224"/>
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373 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
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374 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
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375 </output_collection>
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376 </test>
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377 </tests>
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378 <help><![CDATA[**What it does**
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379 ** Tool input**
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380 abromics_galaxy_json_extractor can use several input type from at least 14 different tools :
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381 | Tools | Version | Default input file| Optional files |
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382 | -: | :-: | :- | :- |
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383 | Abricate | 1.0.1 | output.tsv | |
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384 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt |
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385 | Bandage | 0.8.1 | info.txt | |
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386 | Bracken | 2.8 | output.tsv | taxonomy.tsv |
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387 | Fastp | 0.23.2 | output.json | |
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388 | Integronfinder2| 2.0.2 | output.integrons | output.summary |
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389 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna |
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390 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt |
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391 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta |
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392 | Quast | 5.2.0 | output.tsv | |
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393 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv |
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394 | Refseqmasher | 0.1.2 | output.tsv | |
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395 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa |
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396 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
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397 | tabular_file | 0 | output.tsv | no optional files |
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398
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399 ** Options **
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400 You can add a tool version and a database version for related tools.
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401 For some tools you can add optional files previously produced by the tool
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402 ]]></help>
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403 <expand macro="citations"/>
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404 </tool>