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comparison discosnp_pp.xml @ 0:dc70286127fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author iuc
date Fri, 20 Oct 2017 03:15:43 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="2.2.10">
3 <description>is an efficient tool for detecting SNPs without a reference genome.</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="2.2.10">discosnp</requirement>
9 </requirements>
10 <command><![CDATA[
11 ## simple option
12 #if str( $input_type_options.input_type) == "single"
13 @discosnp_single_reads@
14 ## paired option
15 #else if str( $input_type_options.input_type) == "paired"
16 @discosnp_paired_reads@
17 ## mix option
18 #else
19 @discosnp_single_reads@
20 @discosnp_paired_reads@
21 #end if
22
23 #if str($VCF_option.mapping) == 'reference'
24 #set $reference_file = str($VCF_option.G) + "." + $VCF_option.G.ext
25 ln -sf '${VCF_option.G}' '${reference_file}' &&
26 #end if
27
28 run_discoSnp++.sh
29 -r input.lst
30 -b ${b}
31 -D ${D}
32 -P ${P}
33 ${low_complexity}
34 -k ${k}
35 ${t}
36 ${T}
37
38 #if str($coverage_options_type.coverage_options) == 'auto'
39 -c auto
40 #else
41 -c '${coverage_options_type.c}'
42 #end if
43 -C ${C}
44 -d ${d}
45
46 #if str($VCF_option.mapping) == 'reference'
47 -G '${reference_file}'
48 -M ${VCF_option.M}
49 ${VCF_option.R}
50 #end if
51
52 ]]></command>
53
54 <inputs>
55
56 <conditional name="input_type_options">
57 <param name="input_type" type="select" label="Input options">
58 <option value="single">Single end reads</option>
59 <option value="paired">Paired end reads</option>
60 <option value="mix">Both single and paired reads</option>
61 </param>
62 <when value="single">
63 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
64 </when>
65 <when value="paired">
66 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
67 </when>
68 <when value="mix">
69 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
70 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
71 </when>
72 </conditional>
73
74 <param argument="-b" type="select" label="Branching strategy">
75 <option value="0">variants for which any of the two paths is branching are discarded</option>
76 <option value="1">forbid SNPs for wich the two paths are branching</option>
77 <option value="2">No limitation on branching</option>
78 </param>
79
80 <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp++ will search for deletions of size from 1 to D included"/>
81 <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp++ will search up to P SNPs in a unique bubble"/>
82 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
83 <param argument="-k" type="integer" label="Size of kmers" value="31" />
84
85 <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />
86 <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
87
88
89 <conditional name="coverage_options_type" >
90 <param name="coverage_options" type="select" label="Coverage option">
91 <option value="auto"></option>
92 <option value="custom"></option>
93 </param>
94 <when value="auto" />
95 <when value="custom">
96 <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
97 </when>
98 </conditional>
99
100 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
101 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
102
103 <conditional name="VCF_option" >
104 <param name="mapping" type="select" label="VCF option">
105 <option value="default">Do not use reference genome</option>
106 <option value="reference">Mapping with a reference genome</option>
107 </param>
108 <when value="default"></when>
109 <when value="reference">
110 <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
111 <param argument="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />
112 <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
113 </when>
114 </conditional>
115
116 </inputs>
117
118 <outputs>
119 <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
120 <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
121 </outputs>
122
123 <tests>
124 <test>
125 <conditional name="input_type_options">
126 <param name="input_type" value="single"/>
127 <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />
128 </conditional>
129 <param name="k" value="25"/>
130 <output name="fasta" file="discosnp/multifasta.fa"/>
131 <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
132 </test>
133 <test>
134 <conditional name="input_type_options">
135 <param name="input_type" value="paired"/>
136 <param name="list_paired_reads">
137 <collection type="list:paired">
138 <element name="Pair1">
139 <collection type="paired">
140 <element name="forward" value="discosnp/reads1" ftype="fasta"/>
141 <element name="reverse" value="discosnp/reads2" ftype="fasta"/>
142 </collection>
143 </element>
144 </collection>
145 </param>
146 </conditional>
147 <conditional name="VCF_option">
148 <param name="mapping" value="reference"/>
149 <param name="G" value="discosnp/reads1" ftype="fasta"/>
150 </conditional>
151 <output name="fasta" file="discosnp/multifasta_paired.fa"/>
152 <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
153 </test>
154 </tests>
155
156 <help><![CDATA[
157
158 **Description**
159
160 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
161 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.
162 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.
163
164 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
165
166 -------
167
168 .. class:: warningmark
169
170 **Input parameters**
171
172 -Sequences files in fasta or fastq each allele will be counted in each file individually
173
174 -Use collections: data list and/or data list paired
175
176 -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
177
178 -------
179
180 .. class:: warningmark
181
182 **Ouput parameters**
183
184 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
185
186 -Fasta file with sequence extensions around the SNP.
187
188
189 -------
190
191 **Web site**
192
193 https://colibread.inria.fr/software/discosnp/
194
195 ]]></help>
196 <expand macro="citations">
197 <citation type="doi">10.1093/nar/gku1187</citation>
198 </expand>
199 </tool>