Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

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author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 6837f733b4aa
children
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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="3.0">
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2 <description>performs various 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">perl-bioperl</requirement>
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7 <requirement type="package" version="2.3.5">bowtie2</requirement>
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8 <requirement type="package" version="1.3.1">samtools</requirement>
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9 <requirement type="package" version="1.3.1">bcftools</requirement>
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10 <requirement type="package">bwa</requirement>
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11 <requirement type="package">mmseqs2</requirement>
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12 <requirement type="package">spades</requirement>
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13 <requirement type="package">fastqc</requirement>
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14 <requirement type="package" version="0.2.4">mentalist</requirement>
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15 <requirement type="package" version="3.6.7">ncbi-amrfinderplus</requirement>
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16 </requirements>
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17 <!-- basic error handling -->
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18 <stdio>
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19 <exit_code range="1:" level="fatal" description="Tool exception" />
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20 </stdio>
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21 <command>
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22 python
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23 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci
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24 #if str( $library.type ) == "single":
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25 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
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26 --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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27 --text1 $text_file_1
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28 #elif str( $library.type ) == "paired":
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29 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
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30 --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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31 --text1 $text_file_1
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32 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}'
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33 --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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34 --text2 $text_file_2
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35 #elif str( $library.type ) == "pairedcollection":
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36 -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.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_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.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 #end if
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43 #if $serotyping:
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44 --serotyping
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45 --antigen_O $antigen_O --antigen_H $antigen_H
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46 #end if
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47 #if $virulotyping:
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48 --virulotyping
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49 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
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50 #end if
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51 #if $shigatoxintyping:
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52 --shigatoxintyping
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53 --stx $stx
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54 #end if
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55 #if $amrtyping:
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56 --amrtyping
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57 --amr $amr
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58 --amr_id $__app__.security.encode_id($amr.dataset.id)
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59 #end if
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60 </command>
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61
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62 <inputs>
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63 <!-- single/paired -->
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64 <conditional name="library">
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65 <param name="type" type="select" label="Is this a single-end or paired-end library">
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66 <option value="single">Single-end</option>
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67 <option value="paired">Paired-end</option>
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68 <option value="pairedcollection">Paired-end collection</option>
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69 </param>
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70 <when value="single">
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71 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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72 </when>
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73 <when value="paired">
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74 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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75 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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76 </when>
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77 <when value="pairedcollection">
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78 <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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79 </when>
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80 </conditional>
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81 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
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82 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
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83 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
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84 <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" />
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85 </inputs>
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86
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87 <!-- define outputs -->
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88 <outputs>
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89 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
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90 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" />
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91 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
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92 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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93 </data>
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94 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
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95 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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96 </data>
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97 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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98 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true">
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99 <filter>virulotyping</filter>
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100 </data>
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101 <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" >
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102 <filter>shigatoxintyping</filter>
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103 </data>
3
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104 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" />
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105 <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true">
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106 <filter>serotyping</filter>
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107 </data>
3
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108 <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true">
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109 <filter>serotyping</filter>
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110 </data>
3
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111 <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true">
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112 <filter>amrtyping</filter>
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113 </data>
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114 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 <!-- basic test on contigs file -->
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120 <param name="type" value="single"/>
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121 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
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122 <param name="serotyping" value="true"/>
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123 <output name="report_out">
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124 <assert_contents>
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125 <has_text text="wzx_208_AF529080_O26" />
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126 <has_text text="wzy_192_AF529080_O26" />
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127 <has_text text="fliC_269_AY337465_H11" />
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128 <has_text text="fliC_276_AY337472_H11" />
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129 </assert_contents>
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130 </output>
3
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131 <output name="antigen_O" file="antigen_O" ftype="tabular" />
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132 <output name="antigen_H" file="antigen_H" ftype="tabular" />
0
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133 </test>
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134 </tests>
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135
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136 <help>
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137 **EURL VTEC WGS PT Overview**
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138 This tool performs various typing tools:
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139
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140 - Raw data quality check (FASTQC)
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141
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142 - Trimming (FASTQ positional and quality trimming)
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143
3
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144 - Assembly (SPAdes)
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145
0
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146 - Virulotyping (patho_typing tool from the INNUENDO Project)
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147
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148 - Multi Locus Sequence Typing (MentaLiST 7 loci)
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149
3
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150 - Serotyping (mmseqs2)
0
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151
3
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152 - Shigatoxintyping (mmseqs2 against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU)
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153
3
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154 - AMR typing (AMRFinderPlus)
0
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155
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156 Istituto Superiore di Sanità
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157
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158 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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159
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160 Developer: Arnold Knijn arnold.knijn@iss.it
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161
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162 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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163 ("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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164 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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165 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
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166 </help>
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167 <citations>
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168 <citation type="bibtex">@ARTICLE{andrews_s,
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169 author = {Andrews, S},
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170 keywords = {bioinformatics, ngs, qc},
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171 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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172 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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173 }</citation>
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174 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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175 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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176 <citation type="doi">10.1038/nmeth.1923</citation>
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177 <citation type="doi">10.1099/mgen.0.000146</citation>
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178 <citation type="doi">10.1089/cmb.2012.0021</citation>
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179 <citation type="doi">10.1038/s41467-018-04964-5</citation>
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180 <citation type="doi">10.1128/AAC.00483-19</citation>
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181 <citation type="doi">10.1128/JCM.00008-15</citation>
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182 </citations>
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183 </tool>