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comparison spotyping.xml @ 7:1bf76073c034 draft

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planemo upload
author jowong
date Tue, 13 Nov 2018 03:03:41 -0500
parents 20c20bcdec36
children ff5b31cdc6ba
comparison
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6:20c20bcdec36 7:1bf76073c034
1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.5"> 1 <tool id="spotyping" name="Spoligotype Prediction" version="1.0.0">
2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description> 2 <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1">spotyping</requirement> 4 <requirement type="package" version="2.1">spotyping</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
26 </param> 26 </param>
27 <when value="paired"> 27 <when value="paired">
28 <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"/>
29 </when> 29 </when>
30 <when value="single"> 30 <when value="single">
31 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> 31 <param name="input2" format="data" type="data_collection" label="input" help="Specify dataset with single reads"/>
32 </when> 32 </when>
33 </conditional> 33 </conditional>
34 <section name="advanced" title="Advanced options" expanded="false"> 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" /> 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" /> 36 <param type="boolean" argument="--swift" label="Swift mode" checked="true" truevalue="--swift=on" falsevalue="--swift=off" />
42 <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"/>
43 <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"/>
44 <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"/>
45 </outputs> 45 </outputs>
46 <help><![CDATA[ 46 <help><![CDATA[
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 47 This is a modified version of IUC's wrapper of spotyping without the concatenation and renaming of the input files. The wrapper also runs properly when supplied with paired-end reads
48 48
49 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs. 49 SpoTyping_ is a software for predicting spoligotype_ from sequencing reads, complete genomic sequences and assembled contigs.
50 50
51 **Input:** 51 **Input:**
52 52
60 60
61 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code. 61 Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.
62 62
63 **Options:** 63 **Options:**
64 64
65 \--noQuery
66 Avoid querying the SITVIT_ online service to describe the prevalance of the reported spoligotype.
67 65
68 \--seq 66 \--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] 67 Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]
70 68
71 \-s SWIFT, --swift=SWIFT 69 \-s SWIFT, --swift=SWIFT
72 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping 70 Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping
73 71
74 \--sorted 72 \-m MIN, --min=MIN
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 73 minimum number of error-free hits to support presence of a spacer [Default: 5]
76 to sample reads across positions in the genome evenly. 74
75 \-r MIN_RELAX, --rmin=MIN_RELAX
76 minimum number of 1-error-tolerant hits to support presence of a spacer [Default: 6].
77 77
78 \--filter
79 Filter reads such that:
80 78
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 79
86 **Got weird spoligotype prediction?** 80 **Got weird spoligotype prediction?**
87 81
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. 82 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 83