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comparison tools/spades_2_5/spades.xml @ 7:95ddc2380130 draft

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author lionelguy
date Thu, 28 Nov 2013 05:29:32 -0500
parents d82f18c76309
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6:1b1af74a54ae 7:95ddc2380130
1 <tool id="spades" name="spades" version="0.6"> 1 <tool id="spades" name="spades" version="0.7">
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="2.5.1">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
14 ## Forces unzipped output, faster 14 ## Forces unzipped output, faster
15 --disable-gzip-output 15 --disable-gzip-output
16 $sc 16 $sc
17 $onlyassembler 17 $onlyassembler
18 $careful 18 $careful
19 $rectangles 19 ##$rectangles
20 -t $threads 20 -t \${GALAXY_SLOTS:-16}
21 -k $kmers 21 -k "$kmers"
22 ##-i $iterations 22 ##-i $iterations
23 ##--phred-offset 23 ##--phred-offset
24 ## Sequence files 24 ## Sequence files
25 #for $i, $library in enumerate( $libraries ) 25 #for $i, $library in enumerate( $libraries )
26 #set num=$i+1 26 #set num=$i+1
47 <option value="false">No</option> 47 <option value="false">No</option>
48 <option value="true">Yes</option> 48 <option value="true">Yes</option>
49 </param> 49 </param>
50 <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)" />
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)." /> 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)." />
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)." /> 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)." /> It uses a different format for the sequence identifier in the output FASTA files which do not contain the coverage information -->
53 <param name="threads" type="integer" label="Number of threads to use" value="16"> 53 <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1" /> -->
54 </param>
55 <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> -->
56 <!-- </param> -->
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." > 54 <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." >
58 </param> 55 </param>
59 <!-- Reads --> 56 <!-- Reads -->
60 <repeat name="libraries" title="Libraries"> 57 <repeat name="libraries" title="Libraries" min="1" 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.">
61 <param name="lib_type" type="select" label="Library type"> 58 <param name="lib_type" type="select" label="Library type">
62 <option value="paired_end">Paired end / Single reads</option> 59 <option value="paired_end">Paired-end / Single reads</option>
63 <option value="mate_paired">Mate pairs</option> 60 <option value="mate_paired">Mate pairs</option>
64 </param> 61 </param>
65 <param name="orientation" type="select" label="Orientation"> 62 <param name="orientation" type="select" label="Orientation">
66 <option value="fr" selected="true">-> &lt;- (fr)</option> 63 <option value="fr" selected="true">-> &lt;- (fr)</option>
67 <option value="rf">&lt;- -> (rf)</option> 64 <option value="rf">&lt;- -> (rf)</option>
68 <option value="ff">-> -> (ff)</option> 65 <option value="ff">-> -> (ff)</option>
69 </param> 66 </param>
70 <repeat name="files" title="Files"> 67 <repeat name="files" title="Files" min="1">
71 <conditional name="file_type"> 68 <conditional name="file_type">
72 <param name="type" type="select" label="Select file format"> 69 <param name="type" type="select" label="Select file format">
73 <option value="separate">Separate input files</option> 70 <option value="separate">Separate input files</option>
74 <option value="interleaved">Interleaved files</option> 71 <option value="interleaved">Interleaved files</option>
75 <option value="unpaired">Unpaired/Single reads</option> 72 <option value="unpaired">Unpaired/Single reads</option>
95 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" /> 92 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
96 <data name="out_log" format="txt" label="SPAdes log" /> 93 <data name="out_log" format="txt" label="SPAdes log" />
97 </outputs> 94 </outputs>
98 <!-- <tests> 95 <!-- <tests>
99 <test> 96 <test>
100
101 <param name="sc" value="false" /> 97 <param name="sc" value="false" />
102 <param name="careful" value="false" /> 98 <param name="careful" value="false" />
103 <param name="rectangle" value="false" />
104 <param name="threads" value="16" />
105 <param name="kmers" value="33,55" /> 99 <param name="kmers" value="33,55" />
106 <param name="type" value="pairedend" /> 100 <param name="type" value="pairedend" />
107 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> 101 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
108 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> 102 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
109 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> 103 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
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. 121 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.
128 122
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. 123 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.
130 124
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/. 125 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
126
127 ** Acknowledgments **
128
129 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
130
131 Nicola Soranzo fixed bugs in the 0.6 version.
132 </help> 132 </help>
133 </tool> 133 </tool>