comparison plasmidSPAdes.xml @ 0:27b90e43e2d8 draft

planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
author nml
date Mon, 06 Jun 2016 15:13:06 -0400
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1 <tool id="plasmidspades" name="plasmidspades" version="1.0">
2 <description>genome assembler for plasmids</description>
3 <requirements>
4 <requirement type="package" version="3.8.0">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 fileset is a paired-collection, use the key as the name
14 #if $files[0].file_type.type == "paired-collection":
15 $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 --plasmid
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
38 #set num=1
39 #if str( $lib_type ) == "paired_end":
40 #set prefix = 'pe'
41 #elif str( $lib_type ) == "mate_paired":
42 #set prefix = 'mp'
43 #elif str( $lib_type ) == "nxmate_paired":
44 #set prefix = 'nxmate'
45 #else:
46 #set prefix = 'hqmp'
47 #end if
48 --$prefix$num-$orientation
49 #for $file in $files
50 #if $file.file_type.type == "separate"
51 --$prefix$num-1 fastq:$file.file_type.fwd_reads
52 --$prefix$num-2 fastq:$file.file_type.rev_reads
53 #elif $file.file_type.type == "interleaved"
54 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
55 #elif $file.file_type.type == "unpaired"
56 --$prefix$num-s fastq:$file.file_type.unpaired_reads
57 #elif $file.file_type.type == "paired-collection"
58 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
59 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
60 #end if
61 #end for
62
63 ## PacBio reads
64 #for $i, $pacbiolib in enumerate( $pacbio )
65 --pacbio fastq:$pacbiolib.pacbio_reads
66 #end for
67 ## Nanopore
68 #for $i, $nanoporelib in enumerate( $nanopore )
69 --nanopore fastq:$nanoporelib.nanopore_reads
70 #end for
71 ## Sanger
72 #for $i, $sangerlib in enumerate( $sanger )
73 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads
74 #end for
75 ## Contigs
76 #for $i, $trustedcontigs in enumerate( $trustedcontigs )
77 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs
78 #end for
79 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs )
80 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs
81 #end for
82 </command>
83 <inputs>
84 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
85 <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)." />
86 <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." >
87
88 </param>
89 <conditional name="cov">
90 <param name="state" type="select" label="Coverage Cutoff">
91 <option value="off">Off</option>
92 <option value="value">User Specific</option>
93 <option value="auto">Auto</option>
94 </param>
95 <when value="off">
96 </when>
97 <when value="value">
98 <param name="cutoff" type="float" label="Coverage cutoff value" value="" help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" />
99 </when>
100 <when value="auto">
101 </when>
102 </conditional>
103
104
105
106 <param name="iontorrent" type="boolean" truevalue="--iontorrent" falsevalue="" checked="False" label="Libraries are IonTorrent reads?" />
107 <!-- Reads -->
108
109 <param name="lib_type" type="select" label="Library type">
110 <option value="paired_end">Paired-end / Single reads</option>
111 <option value="mate_paired">Mate pairs</option>
112 <option value="high_mate_paired">High Quality Mate pairs</option>
113 <option value="nxmate_paired">Lucigen NxMate pairs</option>
114 </param>
115 <param name="orientation" type="select" label="Orientation">
116 <option value="fr" selected="true">-> &lt;- (fr)</option>
117 <option value="rf">&lt;- -> (rf)</option>
118 <option value="ff">-> -> (ff)</option>
119 </param>
120 <repeat name="files" title="Files" min="1">
121 <conditional name="file_type">
122 <param name="type" type="select" label="Select file format">
123 <option value="separate">Separate input files</option>
124 <option value="interleaved">Interleaved files</option>
125 <option value="unpaired">Unpaired/Single reads</option>
126 <option value="paired-collection">Paired List Collection</option>
127 </param>
128 <when value="separate">
129 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
130 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
131 </when>
132 <when value="interleaved">
133 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
134 </when>
135 <when value="unpaired">
136 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
137 </when>
138 <when value="paired-collection">
139 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" />
140 </when>
141 </conditional>
142 </repeat>
143
144 <!-- PacBio -->
145 <repeat name="pacbio" title="PacBio CLR reads">
146 <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." />
147 </repeat>
148 <!-- Nanopore -->
149 <repeat name="nanopore" title="Nanopore reads">
150 <param name="nanopore_reads" type="data" format="fastq" label="Nanopore reads." help="FASTQ format. For Nanopore, use single reads above." />
151 </repeat>
152 <!-- Sanger -->
153 <repeat name="sanger" title="Sanger reads">
154 <conditional name="file_type">
155 <param name="type" type="select" label="Select file format" help="No read correction is done on Sanger reads, no need to provide quality information.">
156 <option value="fasta">fasta</option>
157 <option value="fastq">fastq</option>
158 </param>
159 <when value="fasta">
160 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" />
161 </when>
162 <when value="fastq">
163 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" />
164 </when>
165 </conditional>
166 </repeat>
167 <!-- Contigs -->
168 <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.">
169 <conditional name="file_type">
170 <param name="type" type="select" label="Select file format">
171 <option value="fasta">fasta</option>
172 <option value="fastq">fastq</option>
173 </param>
174 <when value="fasta">
175 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" />
176 </when>
177 <when value="fastq">
178 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" />
179 </when>
180 </conditional>
181 </repeat>
182 <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.">
183 <conditional name="file_type">
184 <param name="type" type="select" label="Select file format">
185 <option value="fasta">fasta</option>
186 <option value="fastq">fastq</option>
187 </param>
188 <when value="fasta">
189 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" />
190 </when>
191 <when value="fastq">
192 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" />
193 </when>
194 </conditional>
195 </repeat>
196 </inputs>
197 <outputs>
198 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
199 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
200 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
201 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
202 <data name="out_log" format="txt" label="SPAdes log" />
203 </outputs>
204 <tests>
205 <test>
206 <param name="sc" value="false" />
207 <param name="careful" value="false" />
208 <param name="kmers" value="33,55" />
209 <param name="lib_type" value="paired_end" />
210 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
211 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
212 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
213 </test>
214 </tests>
215 <help>
216 **What it does**
217
218 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.
219
220 This wrapper runs SPAdes 3.8, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
221
222 **License**
223
224 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
225
226 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.
227
228 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.
229
230 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
231
232 ** Acknowledgments **
233
234 Original wrapper developed by Lionel Guy.
235
236 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
237
238 Nicola Soranzo fixed various bugs.
239 </help>
240 <citations>
241 <citation type="doi">10.1089/cmb.2012.0021</citation>
242 </citations>
243 </tool>