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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 33fd10e2e353f61438530103bd21c12695f77652
author iuc
date Wed, 21 Dec 2016 17:58:30 -0500
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1 <tool id="spades" name="SPAdes" version="3.9.0">
2 <description>genome assembler for regular and single-cell projects</description>
3 <requirements>
4 <requirement type="package" version="3.9.0">spades</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command>
10 <![CDATA[
11 ## 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
12 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}
13 #if not $kmer_choice.auto_kmer_choice:
14 -k "$kmer_choice.kmers"
15 #end if
16 #if $cov.state == "auto":
17 --cov-cutoff 'auto'
18 #elif $cov.state == "value":
19 --cov-cutoff '$cov.cutoff'
20 #end if
21 $iontorrent
22 ## Sequence files, libraries
23 #for $i, $library in enumerate( $libraries, start=1 )
24 #if str( $library.lib_type ) == "paired_end":
25 #set prefix = 'pe'
26 #elif str( $library.lib_type ) == "mate_paired":
27 #set prefix = 'mp'
28 #elif str( $library.lib_type ) == "nxmate_paired":
29 #set prefix = 'nxmate'
30 #else:
31 #set prefix = 'hqmp'
32 #end if
33 --$prefix$i-$library.orientation
34 #for $file in $library.files
35 #if $file.file_type.type == "separate"
36 --$prefix$i-1 fastq:$file.file_type.fwd_reads
37 --$prefix$i-2 fastq:$file.file_type.rev_reads
38 #elif $file.file_type.type == "interleaved"
39 --$prefix$i-12 fastq:$file.file_type.interleaved_reads
40 #elif $file.file_type.type == "unpaired"
41 --$prefix$i-s fastq:$file.file_type.unpaired_reads
42 #elif $file.file_type.type == "paired-collection"
43 --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
44 --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
45 #end if
46 #end for
47 #end for
48 #for $read in $pacbio_reads:
49 #if $read:
50 --pacbio fastq:$read
51 #end if
52 #end for
53 #for $read in $nanopore_reads:
54 #if $read:
55 --nanopore fastq:$read
56 #end if
57 #end for
58 #for $read in $sanger_reads:
59 #if $read:
60 --sanger $read.extension:$read
61 #end if
62 #end for
63 #for $contig in $trusted_contigs:
64 #if $contig:
65 --trusted-contigs $contig.extension:$contig
66 #end if
67 #end for
68 #for $contig in $untrusted_contigs:
69 #if $contig:
70 --untrusted-contigs $contig.extension:$contig
71 #end if
72 #end for
73 ]]>
74 </command>
75 <inputs>
76 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
77 <option value="false">No</option>
78 <option value="true">Yes</option>
79 </param>
80 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
81 <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
82 <conditional name="kmer_choice">
83 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
84 <when value="false">
85 <param 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." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
86 </when>
87 <when value="true" />
88 </conditional>
89 <conditional name="cov">
90 <param label="Coverage Cutoff" name="state" type="select">
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 value="value">
97 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
98 </when>
99 <when value="auto" />
100 </conditional>
101 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
102 <repeat 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." min="1" name="libraries" title="Libraries">
103 <param label="Library type" name="lib_type" type="select">
104 <option value="paired_end">Paired-end / Single reads</option>
105 <option value="mate_paired">Mate pairs</option>
106 <option value="high_mate_paired">High Quality Mate pairs</option>
107 <option value="nxmate_paired">Lucigen NxMate pairs</option>
108 </param>
109 <param label="Orientation" name="orientation" type="select">
110 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
111 <option value="rf"><![CDATA[<- -> (rf)]]></option>
112 <option value="ff"><![CDATA[-> -> (ff)]]></option>
113 </param>
114 <repeat min="1" name="files" title="Files">
115 <conditional name="file_type">
116 <param label="Select file format" name="type" type="select">
117 <option value="separate">Separate input files</option>
118 <option value="interleaved">Interleaved files</option>
119 <option value="unpaired">Unpaired/Single reads</option>
120 <option value="paired-collection">Paired List Collection</option>
121 </param>
122 <when value="separate">
123 <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
124 <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
125 </when>
126 <when value="interleaved">
127 <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
128 </when>
129 <when value="unpaired">
130 <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
131 </when>
132 <when value="paired-collection">
133 <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
134 </when>
135 </conditional>
136 </repeat>
137 </repeat>
138 <param optional="true" format="fastq" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
139 <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
140 <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
141 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
142 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
143 </inputs>
144 <outputs>
145 <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" />
146 <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" />
147 <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" />
148 </outputs>
149 <tests>
150 <test>
151 <param name="sc" value="false" />
152 <param name="careful" value="false" />
153 <param name="kmers" value="33" />
154 <param name="lib_type" value="paired_end" />
155 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
156 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
157 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
158 </test>
159 <test>
160 <param name="sc" value="false" />
161 <param name="careful" value="false" />
162 <param name="auto_kmer_choice" value="true" />
163 <param name="lib_type" value="paired_end" />
164 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
165 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
166 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
167 </test>
168 <test>
169 <param name="sc" value="false" />
170 <param name="careful" value="false" />
171 <param name="kmers" value="77" />
172 <param name="lib_type" value="paired_end" />
173 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
174 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
175 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
176 </test>
177 </tests>
178 <help>
179 <![CDATA[
180 **What it does**
181
182 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.
183
184 This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
185
186 **License**
187
188 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
189
190 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.
191
192 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.
193
194 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
195
196 ** Acknowledgments **
197
198 Original wrapper developed by Lionel Guy.
199
200 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
201
202 Nicola Soranzo fixed various bugs.
203 ]]>
204 </help>
205 <citations>
206 <citation type="doi">10.1089/cmb.2012.0021</citation>
207 </citations>
208 </tool>