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comparison 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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1 <tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy0" profile="17.01">
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
3
4 <macros>
5 <token name="@TOOL_VERSION@">2.1</token>
6 </macros>
7
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
10 </requirements>
11
12 <command detect_errors="exit_code"><![CDATA[
13 #set $input_file='input.' + $input.extension
14 ln -s '${input}' $input_file &&
15 SpoTyping.py
16 --noQuery
17 $advanced.seq
18 $advanced.swift
19 $advanced.filter
20 $advanced.sorted
21 $input_file &&
22 cat SpoTyping.log SpoTyping > '${output_txt}'
23 ]]>
24 </command>
25
26 <inputs>
27 <param name="input" type="data" format="fastq,fastq.gz,fasta" label="Sequence reads" />
28 <section name="advanced" title="Advanced options" expanded="false">
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" />
30 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
31 <param type="boolean" argument="--filter" label="Stringent filtering of reads" truevalue="--filter" falsevalue="" checked="false" />
32 <param type="boolean" argument="--sorted" label="Reads are sorted to a reference genome" truevalue="--sorted" falsevalue="" />
33 </section>
34 </inputs>
35
36 <outputs>
37 <data name="output_txt" label="SpoTyping spoligotyping on ${on_string}" format="txt" />
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
43 <output name="output_txt">
44 <assert_contents>
45 <has_text text="1111111111111111101111111111111100001111111" />
46 </assert_contents>
47 </output>
48 </test>
49 </tests>
50
51 <help><![CDATA[
52 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
53
54 **Input:**
55
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)
57 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
58
59 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
60 paired end sequencing of a *M. tuberculosis* genome.
61
62 **Output:**
63
64 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
65
66 **Options:**
67
68 \--seq
69 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
70
71 \-s SWIFT, --swift=SWIFT
72 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
73
74 \--sorted
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
76 to sample reads across positions in the genome evenly.
77
78 \--filter
79 Filter reads such that:
80
81 1. Leading and trailing 'N's would be removed.
82 2. Any read with more than 3 'N's in the middle would be removed.
83 3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given
84 the length of the flanking regions.
85
86 **Got weird spoligotype prediction?**
87
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.
89
90 **Interpreting the spoligotype**
91
92 The binary or octal spoligotype can be used to look up lineage information using a service
93 like `TB Lineage`_.
94
95 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
96 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
97 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
98 ]]>
99 </help>
100
101 <citations>
102 <citation type="doi">10.1186/s13073-016-0270-7</citation>
103 </citations>
104 </tool>