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1 <tool id="rnaspades" name="rnaspades" version="1.0">
2 <description>pipeline for de novo transcriptome assembly from RNA-Seq</description>
3 <requirements>
4 <requirement type="package" version="3.9.0">spades</requirement>
5 </requirements>
6 <command interpreter="perl">spades.pl
7 $out_contigs
8 $out_paths
9 $out_log
10
11 ## if the first fileset is a paired-collection, use the key as the name
12 #if $files[0].file_type.type == "paired-collection":
13 $files[0].file_type.fastq_collection.name
14 #else:
15 NODE
16 #end if
17 ## A real command looks like: spades.py -k 21,33,55,77,99,127 -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
18 spades.py
19 ## Forces unzipped output, faster
20 --disable-gzip-output
21 --rna
22 $onlyassembler
23
24 -t \${GALAXY_SLOTS:-16}
25
26 -k "$kmers"
27
28
29 ## Sequence files
30 #set num=1
31 #if str( $lib_type ) == "paired_end":
32 #set prefix = 'pe'
33 #end if
34 --$prefix$num-$orientation
35 #for $file in $files
36 #if $file.file_type.type == "separate"
37 --$prefix$num-1 fastq:$file.file_type.fwd_reads
38 --$prefix$num-2 fastq:$file.file_type.rev_reads
39 #elif $file.file_type.type == "interleaved"
40 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
41 #elif $file.file_type.type == "paired-collection"
42 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
43 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
44 #end if
45 #end for
46
47
48 </command>
49 <inputs>
50 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
51
52 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="55" help="Recommended to use default of k-mer size of 55. In case your RNA-Seq data set contains long Illumina reads (150 bp and longer) you may try to use longer k-mer size (approximately half of the read length)" />
53 <!-- Reads -->
54
55 <param name="lib_type" type="select" label="Library type">
56 <option value="paired_end">Paired-end</option>
57 </param>
58 <param name="orientation" type="select" label="Orientation">
59 <option value="fr" selected="true">-> &lt;- (fr)</option>
60 <option value="rf">&lt;- -> (rf)</option>
61 <option value="ff">-> -> (ff)</option>
62 </param>
63 <repeat name="files" title="Files" min="1">
64 <conditional name="file_type">
65 <param name="type" type="select" label="Select file format">
66 <option value="separate">Separate input files</option>
67 <option value="interleaved">Interleaved files</option>
68 <option value="paired-collection">Paired List Collection</option>
69 </param>
70 <when value="separate">
71 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
72 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
73 </when>
74 <when value="interleaved">
75 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
76 </when>
77 <when value="paired-collection">
78 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" />
79 </when>
80 </conditional>
81 </repeat>
82
83
84 </inputs>
85 <outputs>
86 <data name="out_contigs" format="fasta" label="rnaSPAdes fasta" />
87 <data name="out_paths" format="txt" label="rnaSPAdes fastg" />
88 <data name="out_log" format="txt" label="SPAdes log" />
89 </outputs>
90 <tests>
91 <test>
92 <param name="kmers" value="55" />
93 <param name="lib_type" value="paired_end" />
94 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
95 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
96 <output name="out_contigs" file="transcripts.fasta" ftype="fasta" compare="re_match" lines_diff="1" />
97 <output name="out_paths" file="transcripts.paths" ftype="txt" compare="re_match" lines_diff="1" />
98 </test>
99 </tests>
100 <help>
101 **What it does**
102
103 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.
104
105 This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a single Fasta file with a corresponding file assembly_graph.fastg.
106
107 **License**
108
109 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
110
111 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.
112
113 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.
114
115 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
116
117 ** Acknowledgments **
118
119 Original wrapper developed by Lionel Guy.
120
121 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
122
123 Nicola Soranzo fixed various bugs.
124 </help>
125 <citations>
126 <citation type="doi">10.1089/cmb.2012.0021</citation>
127 </citations>
128 </tool>