Mercurial > repos > cmonjeau > discosnp_plus_plus

comparison bbric_disco.xml @ 0:1beb3ed9e1e3

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author cmonjeau
date Fri, 05 Jun 2015 11:40:18 -0400
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1 <tool id="discosnp_pp" name="discoSnp++" version="2.1.7">
2 <description>is an efficient tool for detecting SNPs without a reference genome.</description>
3 <requirements>
4 <requirement type="package" version="2.1.7">discoSnp_plus_plus</requirement>
5 <requirement type="package" version="0.6.2">bwa</requirement>
6 </requirements>
7 <command interpreter="python">
8 bbric_disco.py
9 -r ${datfile}
10 -b $branching_bubbles
11 -D $deletions
12 -P $limit_snp
13 #if $low_complexity
14 -l
15 #end if
16 -k $kmer
17 #if (str($extension) == 't'):
18 -t
19 #end if
20 #if (str($extension) == 'T'):
21 -T
22 #end if
23 -c $coverage
24 -C ${maxcoverage}
25 -d $error_threshold
26 #if (str($VCF_option.mapping) == 'reference'):
27 -G ${VCF_option.reference}
28 -M ${VCF_option.mapping_error}
29 #end if
30 </command>
31
32 <inputs>
33 <repeat name="input_list" title="input files" min="1">
34 <param name="input" type="data" format="fasta,fastq,fastq.gz" label="input"/>
35 </repeat>
36
37 <param name="kmer" type="integer" label="Size of kmers" value="31" />
38 <param name="coverage" type="integer" label="Minimal coverage per read set" value="4" />
39 <param name="maxcoverage" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
40 <param name="error_threshold" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
41
42 <param name="branching_bubbles" type="select" label="branching strategy">
43 <option value="0">variants for which any of the two paths is branching are discarded</option>
44 <option value="1">forbid SNPs for wich the two paths are branching</option>
45 <option value="2">No limitation on branching</option>
46 </param>
47
48 <param name="deletions" type="integer" label="deletion size" value="0" help="If different of 0, discoSnp++ will search for deletions of size from 1 to the value included"/>
49 <param name="limit_snp" type="integer" label="maximum SNPs per bubble" value="1" help="discoSnp++ will search up to the value SNPs in a unique bubble"/>
50 <param name="low_complexity" type="boolean" default="False" checked="False" label="accept low complexity bubbles" />
51
52 <param name="extension" type="select" label="extension strategy">
53 <option value="n">extends to 30bp on left and right</option>
54 <option value="t">extends left and right until a polymorphism s found (unitigs)</option>
55 <option value="T">extends left and right using local assembly (contigs)</option>
56 </param>
57 <conditional name="VCF_option" >
58 <param name="mapping" type="select" label="VCF option">
59 <option value="default">Do not use reference genome</option>
60 <option value="reference">Mapping with a reference genome</option>
61 </param>
62 <when value="defaut"></when>
63 <when value="reference">
64 <param name="reference" type="data" format="fasta,fastq" label="Reference genome file" />
65 <param name="mapping_error" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />
66 </when>
67 </conditional>
68
69 </inputs>
70
71 <outputs>
72 <!-- <data name="report" from_work_dir="report.txt" format="txt" label="Output of ${tool.name} on $on_string"/> -->
73 <data name="vcf" from_work_dir="coherent.vcf" format="vcf" label="VCF of ${tool.name} on $on_string"/>
74 <data name="fasta" from_work_dir="coherent.fasta" format="fasta" label="Multifasta of the polymorphisms - ${tool.name} on $on_string"/>
75 </outputs>
76
77 <configfiles>
78 <configfile name="datfile">
79 #for $i, $lib in enumerate ($input_list)
80 ${i}::${lib.input}
81 #end for
82 </configfile>
83 </configfiles>
84 <help>
85
86 **Description**
87
88 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
89 Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
90 The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.
91
92 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
93
94 -------
95
96 .. class:: warningmark
97
98 **Input parameters**
99
100 -Sequences files in fasta, fastq or fastq.gz, each allele will be counted in each file individually
101
102 -Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
103
104 -------
105
106 .. class:: warningmark
107
108 **Ouput parameters**
109
110 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
111
112 -Fasta file with sequence extensions around the SNP.
113
114
115 -------
116
117 **Web site**
118
119 https://colibread.inria.fr/software/discosnp/
120
121 -------
122
123 **Integrated by**
124
125 Cyril Monjeaud and Fabrice Legeai
126
127 GenOuest Bio-informatics Core Facility
128
129 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
130
131 support@genouest.org
132
133 If you use this tool in Galaxy, please cite :
134
135 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
136
137 </help>
138 <citations>
139 <citation type="doi">10.1093/nar/gku1187</citation>
140 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
141 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
142 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
143 booktitle = {JOBIM 2013 Proceedings},
144 year = {2013},
145 url = {https://www.e-biogenouest.org/resources/128},
146 pages = {97-106}
147 }
148 </citation>
149 </citations>
150 </tool>
151