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1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.5">
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2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
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3 <requirements>
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4 <requirement type="package" version="2.1">spotyping</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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6
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7 SpoTyping.py
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8 $advanced.seq
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9 $advanced.swift
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10 --min=$advanced.min
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11 --rmin=$advanced.min_relax
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12 #if str( $data_input.data_selector ) == "paired"
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13 $data_input.input1.forward $data_input.input1.reverse
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14 #end if
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15 #if str( $data_input.data_selector ) == "single"
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16 $data_input.input2
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17 #end if
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18 && cp SITVIT_ONLINE.*.xls spotyping.xls
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19 ]]>
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20 </command>
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21 <inputs>
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22 <conditional name="data_input">
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23 <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
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24 <option value="paired">Paired</option>
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25 <option value="single">Single</option>
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26 </param>
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27 <when value="paired">
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28 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
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29 </when>
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30 <when value="single">
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31 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
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32 </when>
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33 </conditional>
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34 <section name="advanced" title="Advanced options" expanded="false">
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35 <param type="boolean" argument="--seq" label="Input is assembled sequence" help="Input is either a complete genomic sequence or assembled contigs from an isolate" truevalue="--seq" falsevalue="" checked="false" />
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36 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
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37 <param name="min" type="integer" value="5" label="MIN" help="minimum number of error-free hits to support presence of a spacer" />
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38 <param name="min_relax" type="integer" value="6" label="MIN RELAX" help="minimum number of 1-error-tolerant hits to support presence of a spacer " />
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39 </section>
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40 </inputs>
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41 <outputs>
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42 <data name="output1" label="spoligotyping results" format="txt" from_work_dir="SpoTyping"/>
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43 <data name="output2" label="spoligotyping log" format="txt" from_work_dir="SpoTyping.log"/>
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44 <data name="output3" label="query" format="excel.xls" from_work_dir="spotyping.xls"/>
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45 </outputs>
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46 <help><![CDATA[
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47 This is a modified version of IUC's wrapper of spotyping without the concatenation and renaming or input files. The wrapper also runs properly when supplied with paired-end reads
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48
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49 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
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50
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51 **Input:**
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52
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53 - Fastq file - if paired end data is used, you may choose to concatenate paired reads into a single input (e.g. using the cat tool)
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54 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
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55
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56 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
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57 paired end sequencing of a *M. tuberculosis* genome.
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58
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59 **Output:**
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60
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61 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
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62
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63 **Options:**
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64
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65 \--noQuery
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66 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
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67
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68 \--seq
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69 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
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70
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71 \-s SWIFT, --swift=SWIFT
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72 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
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73
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74 \--sorted
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75 Set if input reads are sorted relative to positions on a reference genome. If reads are sorted and swift mode is used, swift mode's sampling is adjusted
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76 to sample reads across positions in the genome evenly.
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77
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78 \--filter
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79 Filter reads such that:
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80
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81 1. Leading and trailing 'N's would be removed.
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82 2. Any read with more than 3 'N's in the middle would be removed.
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83 3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
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84 the length of the flanking regions.
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85
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86 **Got weird spoligotype prediction?**
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87
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88 Sequencing throughput is very low (<40Mbp, for example): SpoTyping may not be able to give accurate prediction due to the relatively low read depth.
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89
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90 **Interpreting the spoligotype**
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91
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92 The binary or octal spoligotype can be used to look up lineage information using a service
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93 like `TB Lineage`_.
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94
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95 **SITVIT reports**
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96
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97 Optionally a report on the detected spoligotype can be retrieved from the SITVIT_ database. If such a report is requested it can also be
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98 illustrated as a (PDF format) plot.
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99
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100 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
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101 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
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102 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
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103 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
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104 ]]></help>
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105 <citations>
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106 <citation type="bibtex">
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107 @misc{githubSpoTyping,
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108 author = {Xia, Eryu},
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109 year = {2016},
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110 title = {SpoTyping},
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111 publisher = {GitHub},
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112 journal = {GitHub repository},
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113 url = {https://github.com/xiaeryu/SpoTyping},
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114 }</citation>
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115 <citation type="doi">10.1186/s13073-016-0270-7</citation>
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116 </citations>
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117 </tool>
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