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comparison spades.xml @ 4:35cb17bd8bf9 draft

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planemo upload commit ba4e93c036a072d6aac883bc1aba55e26256498c
author nml
date Mon, 08 Aug 2016 15:56:56 -0400
parents 6dff6ed33cd7
children 909c315b656d
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3:6dff6ed33cd7 4:35cb17bd8bf9
1 <tool id="spades" name="spades" version="1.3.2"> 1 <tool id="spades" name="spades" version="1.4">
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="3.8.0">spades</requirement> 4 <requirement type="package" version="3.9.0">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
23 $sc 23 $sc
24 $onlyassembler 24 $onlyassembler
25 $careful 25 $careful
26 -t \${GALAXY_SLOTS:-16} 26 -t \${GALAXY_SLOTS:-16}
27 27
28 #if str($kmer_choice.auto_kmer_choice) == 'False': 28 #if not $kmer_choice.auto_kmer_choice:
29 -k "$kmer_choice.kmers" 29 -k "$kmer_choice.kmers"
30 #else 30 #else
31 31
32 #end if 32 #end if
33 33
247 <help> 247 <help>
248 **What it does** 248 **What it does**
249 249
250 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. 250 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.
251 251
252 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. 252 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.
253 253
254 **License** 254 **License**
255 255
256 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. 256 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
257 257