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annotate spotyping.xml @ 1:f82981245fbe draft

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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
author iuc
date Sat, 06 Oct 2018 18:48:35 -0400
parents 545d934aed81
children efa2be6db310
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f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
iuc
parents: 0
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1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01">
0
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2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
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4 <macros>
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f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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5 <import>spotyping_macros.xml</import>
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545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
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10 </requirements>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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11
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12 <command detect_errors="exit_code"><![CDATA[
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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13 #set $input_file='input.' + $input.extension
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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14 ln -s '${input}' $input_file &&
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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15 SpoTyping.py
1
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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16 $advanced.noQuery
0
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17 $advanced.seq
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18 $advanced.swift
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19 $advanced.filter
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20 $advanced.sorted
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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21 $input_file &&
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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22 cat SpoTyping.log SpoTyping > '${output_txt}'
1
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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23 #if $advanced.noQuery != '--noQuery':
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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24 && cp SITVIT_ONLINE.*.xls '${output_xls}'
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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25 #if $advanced.pdf_plot == 'yes':
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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26 && SpoTyping_plot.r '${output_xls}' '${output_pdf}'
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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27 #end if
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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28 #end if
0
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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29 ]]>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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30 </command>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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32 <inputs>
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33 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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34 <section name="advanced" title="Advanced options" expanded="false">
1
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35 <param type="boolean" argument="--noQuery" label="Query SITVIT" truevalue="" falsevalue="--noQuery" checked="false" help="Query SITVIT service for report on spoligotype" />
0
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36 <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" />
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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37 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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38 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
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39 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
1
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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40 <param type="boolean" name="pdf_plot" label="Generate plot from SITVIT report output" truevalue="yes" falsevalue="" />
0
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41 </section>
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42 </inputs>
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43
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44 <outputs>
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45 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
1
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46 <data name="output_xls" label="SpoTyping SITVIT report on ${on_string}" format="excel.xls">
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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47 <filter>advanced['noQuery']</filter>
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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48 </data>
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49 <data name="output_pdf" label="SpoTyping plot from SITVIT report on ${on_string}" format="pdf">
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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50 <filter>advanced['pdf_plot']</filter>
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51 </data>
0
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52 </outputs>
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53
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54 <tests>
1
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55 <test expect_num_outputs="1">
0
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56 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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57 <output name="output_txt">
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58 <assert_contents>
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59 <has_text text="1111111111111111101111111111111100001111111" />
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60 </assert_contents>
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61 </output>
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62 </test>
1
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63 <test expect_num_outputs="2">
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64 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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65 <param name="noQuery" value="" />
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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66 <output name="output_txt">
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67 <assert_contents>
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68 <has_text text="1111111111111111101111111111111100001111111" />
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69 </assert_contents>
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70 </output>
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71 <output name="output_xls">
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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72 <assert_contents>
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73 <has_text text="Spoligotype" />
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74 </assert_contents>
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75 </output>
f82981245fbe planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 867c0f76a8837f14b88200d36eece6ceef065178
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76 </test>
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77 <test expect_num_outputs="3">
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78 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
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79 <param name="noQuery" value="" />
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80 <param name="pdf_plot" value="yes" />
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81 <output name="output_txt">
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82 <assert_contents>
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83 <has_text text="1111111111111111101111111111111100001111111" />
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84 </assert_contents>
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85 </output>
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86 <output name="output_xls">
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87 <assert_contents>
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88 <has_text text="Spoligotype" />
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89 </assert_contents>
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90 </output>
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91 <output name="output_pdf">
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92 <assert_contents>
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93 <has_text text="PDF-1.4" />
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94 </assert_contents>
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95 </output>
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96 </test>
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97
0
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98 </tests>
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99
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100 <help><![CDATA[
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101 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
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102
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103 **Input:**
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104
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105 - 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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106 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
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107
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108 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
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109 paired end sequencing of a *M. tuberculosis* genome.
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110
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111 **Output:**
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112
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113 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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114
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115 **Options:**
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116
1
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117 \--noQuery
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118 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
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119
0
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120 \--seq
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121 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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122
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123 \-s SWIFT, --swift=SWIFT
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124 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
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125
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126 \--sorted
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127 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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128 to sample reads across positions in the genome evenly.
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129
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130 \--filter
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131 Filter reads such that:
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132
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133 1. Leading and trailing 'N's would be removed.
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134 2. Any read with more than 3 'N's in the middle would be removed.
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135 3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
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136 the length of the flanking regions.
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137
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138 **Got weird spoligotype prediction?**
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139
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140 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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141
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142 **Interpreting the spoligotype**
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143
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144 The binary or octal spoligotype can be used to look up lineage information using a service
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145 like `TB Lineage`_.
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146
1
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147 **SITVIT reports**
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148
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149 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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150 illustrated as a (PDF format) plot.
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151
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152 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
0
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153 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
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154 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
1
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155 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
0
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156 ]]>
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157 </help>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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158
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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159 <citations>
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160 <expand macro="spotyping_citation" />
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161 </citations>
545d934aed81 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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162 </tool>