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date Mon, 18 Jan 2016 09:53:28 -0500
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1 <tool id="spades" name="spades" version="1.2">
2 <description>SPAdes genome assembler for regular and single-cell projects</description>
3 <requirements>
4 <requirement type="package" version="3.6.2">spades</requirement>
5 </requirements>
6 <command interpreter="perl">spades.pl
7 $out_contigs
8 $out_contig_stats
9 $out_scaffolds
10 $out_scaffold_stats
11 $out_log
12
13 ## if the first library file is a paired-collection, use the key as the name
14 #if $libraries[0].files[0].file_type.type == "paired-collection":
15 $libraries[0].files[0].file_type.fastq_collection.name
16 #else:
17 NODE
18 #end if
19 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
20 spades.py
21 ## Forces unzipped output, faster
22 --disable-gzip-output
23 $sc
24 $onlyassembler
25 $careful
26 -t \${GALAXY_SLOTS:-16}
27 -k "$kmers"
28
29 #if $cov.state == "auto":
30 --cov-cutoff 'auto'
31 #elif $cov.state == "value":
32 --cov-cutoff '$cov.cutoff'
33 #end if
34
35 $iontorrent
36
37 ## Sequence files, libraries
38 #for $i, $library in enumerate( $libraries )
39 #set num=$i+1
40 #if str( $library.lib_type ) == "paired_end":
41 #set prefix = 'pe'
42 #elif str( $library.lib_type ) == "mate_paired":
43 #set prefix = 'mp'
44 #elif str( $library.lib_type ) == "nxmate_paired":
45 #set prefix = 'nxmate'
46 #else:
47 #set prefix = 'hqmp'
48 #end if
49 --$prefix$num-$library.orientation
50 #for $file in $library.files
51 #if $file.file_type.type == "separate"
52 --$prefix$num-1 fastq:$file.file_type.fwd_reads
53 --$prefix$num-2 fastq:$file.file_type.rev_reads
54 #elif $file.file_type.type == "interleaved"
55 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
56 #elif $file.file_type.type == "unpaired"
57 --$prefix$num-s fastq:$file.file_type.unpaired_reads
58 #elif $file.file_type.type == "paired-collection"
59 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
60 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
61 #end if
62 #end for
63 #end for
64 ## PacBio reads
65 #for $i, $pacbiolib in enumerate( $pacbio )
66 --pacbio fastq:$pacbiolib.pacbio_reads
67 #end for
68 ## Nanopore
69 #for $i, $nanoporelib in enumerate( $nanopore )
70 --nanopore fastq:$nanoporelib.nanopore_reads
71 #end for
72 ## Sanger
73 #for $i, $sangerlib in enumerate( $sanger )
74 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads
75 #end for
76 ## Contigs
77 #for $i, $trustedcontigs in enumerate( $trustedcontigs )
78 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs
79 #end for
80 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs )
81 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs
82 #end for
83 </command>
84 <inputs>
85 <param name="sc" type="boolean" truevalue="--sc" falsevalue="" label="Single-cell?" help="This option is required for MDA (single-cell) data.">
86 <option value="false">No</option>
87 <option value="true">Yes</option>
88 </param>
89 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
90 <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." />
91 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." >
92
93 </param>
94 <conditional name="cov">
95 <param name="state" type="select" label="Coverage Cutoff">
96 <option value="off">Off</option>
97 <option value="value">User Specific</option>
98 <option value="auto">Auto</option>
99 </param>
100 <when value="off">
101 </when>
102 <when value="value">
103 <param name="cutoff" type="float" label="Coverage cutoff value" value="" help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" />
104 </when>
105 <when value="auto">
106 </when>
107 </conditional>
108
109
110
111 <param name="iontorrent" type="boolean" truevalue="--iontorrent" falsevalue="" checked="False" label="Libraries are IonTorrent reads?" />
112 <!-- Reads -->
113 <repeat name="libraries" title="Libraries" min="1" help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided.">
114 <param name="lib_type" type="select" label="Library type">
115 <option value="paired_end">Paired-end / Single reads</option>
116 <option value="mate_paired">Mate pairs</option>
117 <option value="high_mate_paired">High Quality Mate pairs</option>
118 <option value="nxmate_paired">Lucigen NxMate pairs</option>
119 </param>
120 <param name="orientation" type="select" label="Orientation">
121 <option value="fr" selected="true">-> &lt;- (fr)</option>
122 <option value="rf">&lt;- -> (rf)</option>
123 <option value="ff">-> -> (ff)</option>
124 </param>
125 <repeat name="files" title="Files" min="1">
126 <conditional name="file_type">
127 <param name="type" type="select" label="Select file format">
128 <option value="separate">Separate input files</option>
129 <option value="interleaved">Interleaved files</option>
130 <option value="unpaired">Unpaired/Single reads</option>
131 <option value="paired-collection">Paired List Collection</option>
132 </param>
133 <when value="separate">
134 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
135 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
136 </when>
137 <when value="interleaved">
138 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
139 </when>
140 <when value="unpaired">
141 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
142 </when>
143 <when value="paired-collection">
144 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" />
145 </when>
146 </conditional>
147 </repeat>
148 </repeat>
149 <!-- PacBio -->
150 <repeat name="pacbio" title="PacBio CLR reads">
151 <param name="pacbio_reads" type="data" format="fastq" label="PacBio CLR reads." help="FASTQ format. For PacBio pre-corrected or CCS reads, use single reads above." />
152 </repeat>
153 <!-- Nanopore -->
154 <repeat name="nanopore" title="Nanopore reads">
155 <param name="nanopore_reads" type="data" format="fastq" label="Nanopore reads." help="FASTQ format. For Nanopore, use single reads above." />
156 </repeat>
157 <!-- Sanger -->
158 <repeat name="sanger" title="Sanger reads">
159 <conditional name="file_type">
160 <param name="type" type="select" label="Select file format" help="No read correction is done on Sanger reads, no need to provide quality information.">
161 <option value="fasta">fasta</option>
162 <option value="fastq">fastq</option>
163 </param>
164 <when value="fasta">
165 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" />
166 </when>
167 <when value="fastq">
168 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" />
169 </when>
170 </conditional>
171 </repeat>
172 <!-- Contigs -->
173 <repeat name="trustedcontigs" title="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species.">
174 <conditional name="file_type">
175 <param name="type" type="select" label="Select file format">
176 <option value="fasta">fasta</option>
177 <option value="fastq">fastq</option>
178 </param>
179 <when value="fasta">
180 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" />
181 </when>
182 <when value="fastq">
183 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" />
184 </when>
185 </conditional>
186 </repeat>
187 <repeat name="untrustedcontigs" title="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species.">
188 <conditional name="file_type">
189 <param name="type" type="select" label="Select file format">
190 <option value="fasta">fasta</option>
191 <option value="fastq">fastq</option>
192 </param>
193 <when value="fasta">
194 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" />
195 </when>
196 <when value="fastq">
197 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" />
198 </when>
199 </conditional>
200 </repeat>
201 </inputs>
202 <outputs>
203 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
204 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
205 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
206 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
207 <data name="out_log" format="txt" label="SPAdes log" />
208 </outputs>
209 <tests>
210 <test>
211 <param name="sc" value="false" />
212 <param name="careful" value="false" />
213 <param name="kmers" value="33,55" />
214 <param name="lib_type" value="paired_end" />
215 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
216 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
217 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
218 </test>
219 </tests>
220 <help>
221 **What it does**
222
223 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
224
225 This wrapper runs SPAdes 3.6.1, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
226
227 **License**
228
229 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
230
231 This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
232
233 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
234
235 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
236
237 ** Acknowledgments **
238
239 Original wrapper developed by Lionel Guy.
240
241 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
242
243 Nicola Soranzo fixed various bugs.
244 </help>
245 <citations>
246 <citation type="doi">10.1089/cmb.2012.0021</citation>
247 </citations>
248 </tool>