annotate eurl_vtec_wgs_pt.xml @ 6:20ff3dca457f draft default tip

planemo upload commit 6857c749c21f580c828aba3543e294b69d32b662
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date Mon, 23 Oct 2023 11:45:36 +0000
parents 32b5625795ea
children
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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="4.0+galaxy1">
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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="2.23">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 &quot;fastqsanger&quot;" />
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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 &quot;fastqsanger&quot;" />
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83 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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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 &quot;fastqsanger&quot;" 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>