Mercurial > repos > lionelguy > spades
comparison tools/spades_2_5/spades.xml @ 3:d82f18c76309 draft
Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
author | lionelguy |
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date | Thu, 12 Sep 2013 07:46:54 -0400 |
parents | b5ce24f34dd7 |
children | 95ddc2380130 |
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2:b5ce24f34dd7 | 3:d82f18c76309 |
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1 <tool id="spades" name="spades" version="0.5"> | 1 <tool id="spades" name="spades" version="0.6"> |
2 <description>SPAdes genome assembler for regular and single-cell projects</description> | 2 <description>SPAdes genome assembler for regular and single-cell projects</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.5.0">spades</requirement> | 4 <requirement type="package" version="2.5.1">spades</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="perl">spades.pl | 6 <command interpreter="perl">spades.pl |
7 $out_contigs | 7 $out_contigs |
8 $out_contig_stats | 8 $out_contig_stats |
9 $out_scaffolds | 9 $out_scaffolds |
10 $out_scaffold_stats | 10 $out_scaffold_stats |
11 $out_log | 11 $out_log |
12 ## 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 ## 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 |
13 spades.py | 13 spades.py |
14 ## Forces unzipped output, faster | |
15 --disable-gzip-output | |
14 $sc | 16 $sc |
15 $onlyassembler | 17 $onlyassembler |
16 $careful | 18 $careful |
17 $rectangle | 19 $rectangles |
18 -t $threads | 20 -t $threads |
19 -k $kmers | 21 -k $kmers |
20 -i $iterations | 22 ##-i $iterations |
21 ##--phred-offset | 23 ##--phred-offset |
22 ## Sequence files | 24 ## Sequence files |
23 #for $i, $library in enumerate( $libraries ) | 25 #for $i, $library in enumerate( $libraries ) |
24 #set num=$i+1 | 26 #set num=$i+1 |
25 #if str( $library.lib_type ) == "paired_end": | 27 #if str( $library.lib_type ) == "paired_end": |
28 #set prefix = 'mp' | 30 #set prefix = 'mp' |
29 #end if | 31 #end if |
30 --$prefix$num-$library.orientation | 32 --$prefix$num-$library.orientation |
31 #for $file in $library.files | 33 #for $file in $library.files |
32 #if $file.file_type.type == "separate" | 34 #if $file.file_type.type == "separate" |
33 --$prefix$num-1 $file.file_type.fwd_reads | 35 --$prefix$num-1 fastq:$file.file_type.fwd_reads |
34 --$prefix$num-2 $file.file_type.rev_reads | 36 --$prefix$num-2 fastq:$file.file_type.rev_reads |
35 #elif $file.file_type.type == "interleaved" | 37 #elif $file.file_type.type == "interleaved" |
36 --$prefix$num-12 $file.file_type.interleaved_reads | 38 --$prefix$num-12 fastq:$file.file_type.interleaved_reads |
37 #elif $file.file_type.type == "unpaired" | 39 #elif $file.file_type.type == "unpaired" |
38 --$prefix$num-s $file.file_type.unpaired_reads | 40 --$prefix$num-s fastq:$file.file_type.unpaired_reads |
39 #end if | 41 #end if |
40 #end for | 42 #end for |
41 #end for | 43 #end for |
42 </command> | 44 </command> |
43 <inputs> | 45 <inputs> |
45 <option value="false">No</option> | 47 <option value="false">No</option> |
46 <option value="true">Yes</option> | 48 <option value="true">Yes</option> |
47 </param> | 49 </param> |
48 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> | 50 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> |
49 <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)." /> | 51 <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)." /> |
50 <param name="rectangle" type="boolean" truevalue="--rectangle" falsevalue="" checked="False" label="Use rectangle correction for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> | 52 <param name="rectangles" type="boolean" truevalue="--rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> |
51 <param name="threads" type="integer" label="Number of threads to use" value="16"> | 53 <param name="threads" type="integer" label="Number of threads to use" value="16"> |
52 </param> | 54 </param> |
53 <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> | 55 <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> --> |
54 </param> | 56 <!-- </param> --> |
55 <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." > | 57 <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." > |
56 </param> | 58 </param> |
57 <!-- Reads --> | 59 <!-- Reads --> |
58 <repeat name="libraries" title="Libraries"> | 60 <repeat name="libraries" title="Libraries"> |
59 <param name="lib_type" type="select" label="Library type"> | 61 <param name="lib_type" type="select" label="Library type"> |
108 </test> | 110 </test> |
109 </tests> --> | 111 </tests> --> |
110 <help> | 112 <help> |
111 **What it does** | 113 **What it does** |
112 | 114 |
113 Runs SPAdes 2.5.0, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. | 115 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. |
114 | 116 |
115 **Citation** | 117 This wrapper runs SPAdes 2.5.1, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. |
118 | |
119 **SPAdes citation** | |
116 | 120 |
117 Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021. | 121 Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021. |
118 | 122 |
123 **License** | |
124 | |
125 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. | |
126 | |
127 This wrapper is copyrighted by Lionel Guy, 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. | |
128 | |
129 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. | |
130 | |
131 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. | |
119 </help> | 132 </help> |
120 </tool> | 133 </tool> |