Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate eurl_vtec_wgs_pt.xml @ 2:65378117a8c0 draft
planemo upload commit cd404de897dc786471b6ea98f9dda612501b2469
author | iss |
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date | Thu, 19 Oct 2023 11:19:56 +0000 |
parents | 444b0421bbdc |
children | 32b5625795ea |
rev | line source |
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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="4.0"> |
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2 <description>workflow that performs various E. coli typing tools</description> |
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3 <requirements> |
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4 <requirement type="package" version="3.7">python</requirement> |
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5 <requirement type="package" version="5.26">perl</requirement> |
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6 <requirement type="package" version="1.7">perl-bioperl</requirement> |
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7 <requirement type="package" version="0.39">trimmomatic</requirement> |
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8 <requirement type="package" version="8.25">coreutils</requirement> |
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9 <requirement type="package" version="2.3.4">bowtie2</requirement> |
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10 <requirement type="package" version="1.3.1">samtools</requirement> |
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11 <requirement type="package" version="1.3.1">bcftools</requirement> |
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12 <requirement type="package" version="0.7.17">bwa</requirement> |
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13 <requirement type="package" version="3.15">spades</requirement> |
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14 <requirement type="package" version="2.3">skesa</requirement> |
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15 <requirement type="package" version="0.11.9">fastqc</requirement> |
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16 <requirement type="package" version="5.0.2">quast</requirement> |
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17 <requirement type="package" version="3.8">muscle</requirement> |
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18 <requirement type="package" version="2.19">mlst</requirement> |
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19 <requirement type="package" version="1.0.1">abricate</requirement> |
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20 <requirement type="package" version="2020.2">tbb</requirement> |
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21 </requirements> |
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22 <!-- basic error handling --> |
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23 <stdio> |
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24 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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25 </stdio> |
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26 <command> |
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27 <![CDATA[ |
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28 python |
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29 $__tool_directory__/EURL_VTEC_WGS_PT.py --base_url $__app__.config.galaxy_infrastructure_url --log $logfile --output $report_out |
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30 --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci |
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31 #if str( $library.type ) == "single": |
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32 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' |
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33 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} |
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34 --text1 $text_file_1 |
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35 #elif str( $library.type ) == "paired": |
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36 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' |
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37 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} |
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38 --text1 $text_file_1 |
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39 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}' |
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40 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} |
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41 --text2 $text_file_2 |
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42 #elif str( $library.type ) == "pairedcollection": |
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43 -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}' |
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44 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} |
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45 --text1 $text_file_1 |
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46 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}' |
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47 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} |
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48 --text2 $text_file_2 |
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49 #end if |
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50 #if $serotyping: |
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51 --serotyping |
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52 --antigen_O $antigen_O --antigen_H $antigen_H |
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53 #end if |
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54 #if $virulotyping: |
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55 --virulotyping |
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56 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id) |
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57 #end if |
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58 #if $shigatoxintyping: |
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59 --shigatoxintyping |
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60 --stx $stx |
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61 #end if |
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62 #if $amrtyping: |
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63 --amrtyping |
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64 --amr $amr |
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65 --amr_id $__app__.security.encode_id($amr.dataset.id) |
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66 #end if |
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67 ]]> |
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68 </command> |
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69 |
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70 <inputs> |
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71 <!-- single/paired --> |
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72 <conditional name="library"> |
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73 <param name="type" type="select" label="Is this a single-end or paired-end library"> |
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74 <option value="single">Single-end</option> |
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75 <option value="paired">Paired-end</option> |
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76 <option value="pairedcollection">Paired-end collection</option> |
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77 </param> |
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78 <when value="single"> |
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79 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> |
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80 </when> |
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81 <when value="paired"> |
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82 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> |
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83 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> |
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84 </when> |
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85 <when value="pairedcollection"> |
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86 <param name="input_pc" type="data_collection" label="Paired-end FASTQ collection" help="Must be of datatype "fastqsanger"" optional="false" format="txt" collection_type="paired" /> |
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87 </when> |
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88 </conditional> |
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89 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" /> |
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90 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" /> |
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91 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" /> |
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92 <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" /> |
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93 </inputs> |
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94 |
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95 <!-- define outputs --> |
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96 <outputs> |
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97 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" /> |
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98 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" /> |
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99 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true"> |
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100 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> |
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101 </data> |
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102 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true"> |
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103 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> |
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104 </data> |
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105 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: contigs" /> |
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106 <data format="tsv" name="quast" label="Quast on ${on_string}" hidden="true" /> |
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107 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true"> |
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108 <filter>virulotyping</filter> |
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109 </data> |
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110 <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" > |
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111 <filter>shigatoxintyping</filter> |
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112 </data> |
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113 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" /> |
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114 <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true"> |
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115 <filter>serotyping</filter> |
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116 </data> |
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117 <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true"> |
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118 <filter>serotyping</filter> |
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119 </data> |
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120 <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true"> |
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121 <filter>amrtyping</filter> |
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122 </data> |
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123 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> |
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124 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data> |
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125 </outputs> |
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126 |
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127 <tests> |
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128 <test> |
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129 <!-- basic test on contigs file --> |
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130 <param name="type" value="single"/> |
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131 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/> |
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132 <param name="serotyping" value="true"/> |
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133 <output name="report_out"> |
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134 <assert_contents> |
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135 <has_text text="wzx_208_AF529080_O26" /> |
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136 <has_text text="wzy_192_AF529080_O26" /> |
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137 <has_text text="fliC_269_AY337465_H11" /> |
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138 <has_text text="fliC_276_AY337472_H11" /> |
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139 </assert_contents> |
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140 </output> |
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141 <output name="antigen_O" file="antigen_O" ftype="tabular" /> |
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142 <output name="antigen_H" file="antigen_H" ftype="tabular" /> |
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143 </test> |
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144 </tests> |
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145 |
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146 <help> |
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147 **EURL VTEC WGS PT Overview** |
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148 This tool performs various typing tools: |
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149 |
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150 - Raw data quality check (FASTQC) |
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151 |
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152 - Trimming (Trimmomatic) |
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153 |
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154 - Assembly (SPAdes) |
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155 |
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156 - Virulotyping (patho_typing tool from the INNUENDO Project) |
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157 |
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158 - Multi Locus Sequence Typing (MLST 7 loci) |
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159 |
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160 - Serotyping (blastn) |
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161 |
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162 - Shigatoxintyping (blastn of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU) |
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163 |
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164 - AMR typing (Abricate with ResFinder database) |
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165 |
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166 Istituto Superiore di Sanità |
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167 |
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168 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) |
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169 |
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170 Developer: Arnold Knijn arnold.knijn@iss.it |
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171 |
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172 The development of the Virulotyping tool has been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 |
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173 ("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento” |
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174 from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014) |
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175 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)]. |
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176 </help> |
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177 <citations> |
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178 <citation type="bibtex">@ARTICLE{andrews_s, |
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179 author = {Andrews, S}, |
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180 keywords = {bioinformatics, ngs, qc}, |
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181 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}}, |
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182 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/} |
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183 }</citation> |
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184 <citation type="doi">10.1093/bioinformatics/btu170</citation> |
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185 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> |
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186 <citation type="doi">10.1038/nmeth.1923</citation> |
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187 <citation type="bibtex">@ARTICLE{seemann_t, |
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188 author = {Seemann, T}, |
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189 keywords = {bioinformatics, ngs}, |
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190 title = {{mlst}}, |
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191 url = {https://github.com/tseemann/mlst/} |
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192 }</citation> |
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193 <citation type="bibtex">@ARTICLE{seemann_t, |
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194 author = {Seemann, T}, |
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195 keywords = {bioinformatics, ngs}, |
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196 title = {{abricate}}, |
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197 url = {https://github.com/tseemann/abricate/} |
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198 }</citation> |
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199 <citation type="doi">10.1089/cmb.2012.0021</citation> |
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200 <citation type="doi">10.1186/s13059-018-1540-z</citation> |
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201 <citation type="doi">d10.1093/jac/dks261</citation> |
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202 <citation type="doi">10.1128/JCM.00008-15</citation> |
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203 <citation type="bibtex">@ARTICLE{andrews_s, |
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204 author = {Li, M, Copeland, A, and Han, J}, |
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205 keywords = {bioinformatics, ngs}, |
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206 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}}, |
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207 url = {https://www.osti.gov/servlets/purl/1016000/} |
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208 }</citation> |
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209 <citation type="bibtex">@ARTICLE{andrews_s, |
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210 author = {Edwards, RA}, |
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211 keywords = {bioinformatics, ngs}, |
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212 title = {{fastq-pair}}, |
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213 url = {https://github.com/linsalrob/EdwardsLab/} |
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214 }</citation> |
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215 <citation type="doi">10.1186/1471-2105-10-421</citation> |
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216 <citation type="doi">10.1093/nar/gkh340</citation> |
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217 </citations> |
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218 </tool> |