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comparison spotyping.xml @ 6:20c20bcdec36 draft

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planemo upload
author jowong
date Tue, 13 Nov 2018 02:50:56 -0500
parents f1b3a263dd3a
children 1bf76073c034
comparison
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5:f1b3a263dd3a 6:20c20bcdec36
1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.4"> 1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.5">
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="2.1">spotyping</requirement> 4 <requirement type="package" version="2.1">spotyping</requirement>
4 </requirements> 5 </requirements>
5 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
6 SpoTyping.py 7 SpoTyping.py
8 $advanced.seq
9 $advanced.swift
10 --min=$advanced.min
11 --rmin=$advanced.min_relax
7 #if str( $data_input.data_selector ) == "paired" 12 #if str( $data_input.data_selector ) == "paired"
8 $data_input.input1.forward $data_input.input1.reverse 13 $data_input.input1.forward $data_input.input1.reverse
9 #end if 14 #end if
10 #if str( $data_input.data_selector ) == "single" 15 #if str( $data_input.data_selector ) == "single"
11 $data_input.input2.element_identifier 16 $data_input.input2
12 #end if 17 #end if
13 && cp SITVIT_ONLINE.*.xls spotyping.xls 18 && cp SITVIT_ONLINE.*.xls spotyping.xls
14 ]]> 19 ]]>
15 </command> 20 </command>
16 <inputs> 21 <inputs>
17 <conditional name="data_input"> 22 <conditional name="data_input">
18 <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"> 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">
19 <option value="paired">Paired</option> 24 <option value="paired">Paired</option>
20 <option value="single">Single</option> 25 <option value="single">Single</option>
21 </param> 26 </param>
22 <when value="paired"> 27 <when value="paired">
23 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/> 28 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
24 </when> 29 </when>
25 <when value="single"> 30 <when value="single">
26 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> 31 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
27 </when> 32 </when>
28 </conditional> 33 </conditional>
34 <section name="advanced" title="Advanced options" expanded="false">
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" />
36 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
37 <param name="min" type="integer" value="5" label="MIN" help="minimum number of error-free hits to support presence of a spacer" />
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 " />
39 </section>
29 </inputs> 40 </inputs>
30 <outputs> 41 <outputs>
31 <data name="output1" label="spoligotyping results" format="txt" from_work_dir="SpoTyping"/> 42 <data name="output1" label="spoligotyping results" format="txt" from_work_dir="SpoTyping"/>
32 <data name="output2" label="spoligotyping log" format="txt" from_work_dir="SpoTyping.log"/> 43 <data name="output2" label="spoligotyping log" format="txt" from_work_dir="SpoTyping.log"/>
33 <data name="output3" label="query" format="excel.xls" from_work_dir="spotyping.xls"/> 44 <data name="output3" label="query" format="excel.xls" from_work_dir="spotyping.xls"/>
34 </outputs> 45 </outputs>
35 <help><![CDATA[ 46 <help><![CDATA[
36 Usage: python SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional) 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
48
49 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
50
51 **Input:**
52
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)
54 - Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)
55
56 *Note on input size*: In swift mode the sampling threshold is reached in approximately 30x coverage when using
57 paired end sequencing of a *M. tuberculosis* genome.
58
59 **Output:**
60
61 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
62
63 **Options:**
64
65 \--noQuery
66 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
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 **SITVIT reports**
96
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
98 illustrated as a (PDF format) plot.
99
100 .. _SpoTyping: https://github.com/xiaeryu/SpoTyping
101 .. _spoligotype: https://www.ncbi.nlm.nih.gov/pubmed/19521871
102 .. _TB Lineage: http://tbinsight.cs.rpi.edu/run_tb_lineage.html
103 .. _SITVIT: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE/
37 ]]></help> 104 ]]></help>
38 <citations> 105 <citations>
39 <citation type="bibtex"> 106 <citation type="bibtex">
40 @misc{githubSpoTyping, 107 @misc{githubSpoTyping,
41 author = {Xia, Eryu}, 108 author = {Xia, Eryu},
43 title = {SpoTyping}, 110 title = {SpoTyping},
44 publisher = {GitHub}, 111 publisher = {GitHub},
45 journal = {GitHub repository}, 112 journal = {GitHub repository},
46 url = {https://github.com/xiaeryu/SpoTyping}, 113 url = {https://github.com/xiaeryu/SpoTyping},
47 }</citation> 114 }</citation>
115 <citation type="doi">10.1186/s13073-016-0270-7</citation>
48 </citations> 116 </citations>
49 </tool> 117 </tool>