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author cstrittmatter
date Mon, 20 Jan 2020 11:05:48 -0500
parents c8c0131be526
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1 <tool id="ecoliserotyper" name="E coli Serotyper" version="1.2">
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2 <description>performs serotyping of Escherichia coli test
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="3.7">python</requirement>
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6 <requirement type="package" version="1.4">scipy</requirement>
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7 <requirement type="package" version="5.26">perl</requirement>
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8 <requirement type="package" version="1.7.2">perl-bioperl</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="0.7.8">bwa</requirement>
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13 <requirement type="package" version="2.7.1">blast</requirement>
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14 <requirement type="package" version="3.12.0">spades</requirement>
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15 <requirement type="package" version="0.11.8">fastqc</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__/Ecoli_Serotyper.py --input_type ${origin.input_type} --log $logfile --output $report_out --blastn_O $blastn_O --blastn_H $blastn_H
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24 #if str( $origin.input_type ) == "contigs":
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25 -1 $origin.input_1 --input1_name '$origin.input_1.name'
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26 #else:
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27 -1 $origin.library.input_1 --input1_ext ${origin.library.input_1.ext} --input1_name '${origin.library.input_1.name}'
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28 --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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29 --spades_log $spades_log
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30 #if str( $origin.library.type ) == "paired":
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31 -2 $origin.library.input_2 --input2_ext ${origin.library.input_2.ext} --input2_name '${origin.library.input_2.name}'
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32 --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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33 #end if
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34 #end if
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35 </command>
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36
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37 <inputs>
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38 <!-- fastq/contigs -->
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39 <conditional name="origin">
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40 <param name="input_type" type="select" label="Are the input files FASTQ or Contigs">
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41 <option value="fastq">FASTQ</option>
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42 <option value="contigs">Contigs</option>
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43 </param>
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44
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45 <when value="fastq">
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46 <!-- single/paired -->
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47 <conditional name="library">
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48 <param name="type" type="select" label="Is this single or paired library">
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49 <option value="single">Single-end</option>
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50 <option value="paired">Paired-end</option>
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51 </param>
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52
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53 <when value="single">
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54 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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55 </when>
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56 <when value="paired">
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57 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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58 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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59 </when>
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60 </conditional>
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61 </when>
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62 <when value="contigs">
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63 <param name="input_1" format="fasta" type="data" label="FASTA Contigs file" help="Must be of datatype &quot;fasta&quot;" />
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64 </when>
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65 </conditional>
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66 </inputs>
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67
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68 <!-- define outputs -->
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69 <outputs>
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70 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true">
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71 <filter>origin['input_type'] == 'fastq'</filter>
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72 </data>
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73 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
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74 <filter>origin['input_type'] == 'fastq' and origin['library']['type'] == 'paired'</filter>
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75 </data>
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76 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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77 <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
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78 <filter>origin['input_type'] == 'fastq'</filter>
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79 </data>
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80 <data name="blastn_O" format="tabular" label="Blastn for O" hidden="true" />
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81 <data name="blastn_H" format="tabular" label="Blastn for H" hidden="true" />
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82 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
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83 </outputs>
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84
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85 <tests>
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86 <test>
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87 <!-- basic test on contigs file -->
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88 <param name="input_type" value="contigs"/>
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89 <param name="input_1" value="a_contigs.fasta" ftype="fasta"/>
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90 <param name="input1_name" value="a_contigs.fasta"/>
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91 <output name="report_out">
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92 <assert_contents>
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93 <has_text text="wzx_208_AF529080_O26" />
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94 <has_text text="wzy_192_AF529080_O26" />
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95 <has_text text="fliC_269_AY337465_H11" />
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96 <has_text text="fliC_276_AY337472_H11" />
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97 </assert_contents>
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98 </output>
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99 <output name="blastn_O" file="blastn_O" ftype="tabular" />
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100 <output name="blastn_H" file="blastn_H" ftype="tabular" />
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101 </test>
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102 </tests>
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103
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104 <help>
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105 **E coli Serotyper Overview**
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106
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107 This tool performs various operations:
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108
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109 - Optionally: Quality assessment (FastQC)
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110
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111 - Optionally: Trimming (FASTQ positional and quality trimming)
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112
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113 - Optionally: Filtering (DUK)
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114
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115 - Optionally: Assembly (SPAdes)
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116
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117 - Serotyping (Blast+ against serotype databases from the Center for Genomic Epidemiology CGE)
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118
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119 Istituto Superiore di Sanita'
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120
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121 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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122
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123 Developer: Arnold Knijn arnold.knijn@iss.it
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124
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125 </help>
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126 <citations>
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127 <citation type="bibtex">@ARTICLE{andrews_s,
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128 author = {Andrews, S},
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129 keywords = {bioinformatics, ngs, qc},
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130 priority = {2},
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131 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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132 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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133 }</citation>
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134 <citation type="bibtex">@ARTICLE{andrews_s,
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135 author = {Li, M, Copeland, A, and Han, J},
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136 keywords = {bioinformatics, ngs},
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137 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
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138 url = {https://www.osti.gov/servlets/purl/1016000/}
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139 }</citation>
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140 <citation type="bibtex">@ARTICLE{andrews_s,
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141 author = {Edwards, RA},
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142 keywords = {bioinformatics, ngs},
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143 title = {{fastq-pair}},
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144 url = {https://github.com/linsalrob/EdwardsLab/}
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145 }</citation>
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146 <citation type="doi">10.1089/cmb.2012.0021</citation>
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147 <citation type="doi">10.1186/1471-2105-10-421</citation>
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148 <citation type="doi">10.1186/s13742-015-0080-7</citation>
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149 <citation type="doi">10.1128/JCM.00008-15</citation>
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150 </citations>
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151 </tool>