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annotate spotyping.xml @ 0:d55b070fc235 draft

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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
author iuc
date Tue, 08 May 2018 10:21:44 -0400
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children ee9f908ce860
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d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
iuc
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1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy0" profile="17.01">
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
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3
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4 <macros>
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5 <token name="@TOOL_VERSION@">2.1</token>
d55b070fc235 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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7
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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>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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11
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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12 <command detect_errors="exit_code"><![CDATA[
d55b070fc235 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.' + $input.extension
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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14 ln -s '${input}' $input_file &&
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15 SpoTyping.py
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16 --noQuery
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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
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21 $input_file &&
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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22 cat SpoTyping.log SpoTyping > '${output_txt}'
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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23 ]]>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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24 </command>
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25
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26 <inputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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27 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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28 <section name="advanced" title="Advanced options" expanded="false">
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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29 <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" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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30 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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31 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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32 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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33 </section>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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34 </inputs>
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35
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36 <outputs>
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37 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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38 </outputs>
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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39
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40 <tests>
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41 <test>
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42 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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43 <output name="output_txt">
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44 <assert_contents>
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45 <has_text text="1111111111111111101111111111111100001111111" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
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50
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51 <help><![CDATA[
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52 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
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53
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54 **Input:**
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55
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56 - 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)
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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57 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
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58
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59 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
d55b070fc235 planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 71c2659a468b7d83f0d438ca6dc888bd8d66d3f5
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60 paired end sequencing of a *M. tuberculosis* genome.
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61
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62 **Output:**
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64 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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65
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66 **Options:**
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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 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
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96 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
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97 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
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98 ]]>
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99 </help>
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100
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101 <citations>
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102 <citation type="doi">10.1186/s13073-016-0270-7</citation>
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103 </citations>
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104 </tool>