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author cstrittmatter
date Wed, 22 Jan 2020 09:10:12 -0500
parents bf3194a789a2
children 0cbed1c0a762
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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3">
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2 <description>performs various typing tools test cfsan
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package">scipy</requirement>
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7 <requirement type="package">perl-bioperl</requirement>
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8 <requirement type="package" version="2.3.5">bowtie2</requirement>
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9 <requirement type="package" version="1.3.1">samtools</requirement>
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10 <requirement type="package" version="1.3.1">bcftools</requirement>
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11 <requirement type="package">bwa</requirement>
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12 <requirement type="package">blast</requirement>
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13 <requirement type="package">spades</requirement>
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14 <requirement type="package">fastqc</requirement>
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15 <requirement type="package">mentalist</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 --trimmed1 $trimmed1
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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 --trimmed1 $trimmed1
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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 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
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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 --trimmed1 $trimmed1
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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 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
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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 --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_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 --blastn_STX $blastn_STX
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54 #end if
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55 </command>
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56
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57 <inputs>
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58 <!-- single/paired -->
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59 <conditional name="library">
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60 <param name="type" type="select" label="Is this a single-end or paired-end library">
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61 <option value="single">Single-end</option>
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62 <option value="paired">Paired-end</option>
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63 <option value="pairedcollection">Paired-end collection</option>
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64 </param>
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65 <when value="single">
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66 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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67 </when>
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68 <when value="paired">
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69 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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70 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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71 </when>
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72 <when value="pairedcollection">
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73 <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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74 </when>
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75 </conditional>
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76 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
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77 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
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78 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
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79 </inputs>
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80
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81 <!-- define outputs -->
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82 <outputs>
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83 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
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84 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" />
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85 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
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86 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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87 </data>
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88 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
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89 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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90 </data>
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91 <data name="trimmed1" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed
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92 #if str( $library.type ) == 'paired'#
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93 forward
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94 #end if#
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95 FASTQ">
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96 </data>
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97 <data name="trimmed2" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed reverse FASTQ">
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98 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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99 </data>
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100 <data name="trimmedunpaired" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed unpaired reads">
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101 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
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102 </data>
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103 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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104 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true">
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105 <filter>virulotyping</filter>
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106 </data>
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107 <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" >
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108 <filter>shigatoxintyping</filter>
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109 </data>
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110 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" />
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111 <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
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112 <filter>serotyping</filter>
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113 </data>
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114 <data name="blastn_O" format="tabular" label="Blastn for O 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="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true">
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118 <filter>serotyping</filter>
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119 </data>
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120 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
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121 </outputs>
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122
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123 <tests>
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124 <test>
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125 <!-- basic test on contigs file -->
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126 <param name="type" value="single"/>
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127 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
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128 <param name="serotyping" value="true"/>
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129 <output name="report_out">
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130 <assert_contents>
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131 <has_text text="wzx_208_AF529080_O26" />
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132 <has_text text="wzy_192_AF529080_O26" />
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133 <has_text text="fliC_269_AY337465_H11" />
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134 <has_text text="fliC_276_AY337472_H11" />
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135 </assert_contents>
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136 </output>
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137 <output name="blastn_O" file="blastn_O" ftype="tabular" />
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138 <output name="blastn_H" file="blastn_H" ftype="tabular" />
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139 </test>
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140 </tests>
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141
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142 <help>
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143 **EURL VTEC WGS PT Overview**
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144 This tool performs various typing tools:
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145
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146 - Raw data quality check (FASTQC)
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147
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148 - Trimming (FASTQ positional and quality trimming)
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149
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150 - Virulotyping (patho_typing tool from the INNUENDO Project)
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151
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152 - Multi Locus Sequence Typing (MentaLiST 7 loci)
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153
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154 - Filtering (DUK)
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155
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156 - Assembly (SPAdes)
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157
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158 - Serotyping (blastn)
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159
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160 - Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU)
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161
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162 Istituto Superiore di Sanità
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163
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164 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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165
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166 Developer: Arnold Knijn arnold.knijn@iss.it
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167
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168 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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169 ("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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170 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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171 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
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172 </help>
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173 <citations>
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174 <citation type="bibtex">@ARTICLE{andrews_s,
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175 author = {Andrews, S},
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176 keywords = {bioinformatics, ngs, qc},
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177 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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178 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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179 }</citation>
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180 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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181 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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182 <citation type="doi">10.1038/nmeth.1923</citation>
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183 <citation type="doi">10.1099/mgen.0.000146</citation>
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184 <citation type="bibtex">@ARTICLE{li-copeland,
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185 author = {Li, M, Copeland, A, and Han, J},
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186 keywords = {bioinformatics, ngs},
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187 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
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188 url = {https://www.osti.gov/servlets/purl/1016000/}
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189 }</citation>
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190 <citation type="bibtex">@ARTICLE{edwards_ra,
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191 author = {Edwards, RA},
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192 keywords = {bioinformatics, ngs},
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193 title = {{fastq-pair}},
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194 url = {https://github.com/linsalrob/EdwardsLab/}
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195 }</citation>
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196 <citation type="doi">10.1089/cmb.2012.0021</citation>
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197 <citation type="doi">10.1186/1471-2105-10-421</citation>
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198 <citation type="doi">10.1186/s13742-015-0080-7</citation>
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199 <citation type="doi">10.1128/JCM.00008-15</citation>
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200 </citations>
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201 </tool>