Mercurial > repos > lionelguy > spades
annotate tools/spades_2_5/spades.xml @ 2:b5ce24f34dd7 draft
Uploaded
| author | lionelguy |
|---|---|
| date | Thu, 05 Sep 2013 07:43:48 -0400 |
| parents | 0f8b2da62d7d |
| children | d82f18c76309 |
| rev | line source |
|---|---|
| 2 | 1 <tool id="spades" name="spades" version="0.5"> |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
2 <description>SPAdes genome assembler for regular and single-cell projects</description> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
3 <requirements> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
4 <requirement type="package" version="2.5.0">spades</requirement> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
5 </requirements> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
6 <command interpreter="perl">spades.pl |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
7 $out_contigs |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
8 $out_contig_stats |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
9 $out_scaffolds |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
10 $out_scaffold_stats |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
11 $out_log |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
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 |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
13 spades.py |
| 2 | 14 $sc |
| 15 $onlyassembler | |
| 16 $careful | |
| 17 $rectangle | |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
18 -t $threads |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
19 -k $kmers |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
20 -i $iterations |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
21 ##--phred-offset |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
22 ## Sequence files |
| 2 | 23 #for $i, $library in enumerate( $libraries ) |
| 24 #set num=$i+1 | |
| 25 #if str( $library.lib_type ) == "paired_end": | |
| 26 #set prefix = 'pe' | |
| 27 #else: | |
| 28 #set prefix = 'mp' | |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
29 #end if |
| 2 | 30 --$prefix$num-$library.orientation |
| 31 #for $file in $library.files | |
| 32 #if $file.file_type.type == "separate" | |
| 33 --$prefix$num-1 $file.file_type.fwd_reads | |
| 34 --$prefix$num-2 $file.file_type.rev_reads | |
| 35 #elif $file.file_type.type == "interleaved" | |
| 36 --$prefix$num-12 $file.file_type.interleaved_reads | |
| 37 #elif $file.file_type.type == "unpaired" | |
| 38 --$prefix$num-s $file.file_type.unpaired_reads | |
| 39 #end if | |
| 40 #end for | |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
41 #end for |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
42 </command> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
43 <inputs> |
| 2 | 44 <param name="sc" type="boolean" truevalue="--sc" falsevalue="" label="Single-cell?" help="This option is required for MDA (single-cell) data."> |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
45 <option value="false">No</option> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
46 <option value="true">Yes</option> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
47 </param> |
| 2 | 48 <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)." /> | |
| 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)." /> | |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
51 <param name="threads" type="integer" label="Number of threads to use" value="16"> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
52 </param> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
53 <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
54 </param> |
| 2 | 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." > |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
56 </param> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
57 <!-- Reads --> |
| 2 | 58 <repeat name="libraries" title="Libraries"> |
| 59 <param name="lib_type" type="select" label="Library type"> | |
| 60 <option value="paired_end">Paired end / Single reads</option> | |
| 61 <option value="mate_paired">Mate pairs</option> | |
| 62 </param> | |
| 63 <param name="orientation" type="select" label="Orientation"> | |
| 64 <option value="fr" selected="true">-> <- (fr)</option> | |
| 65 <option value="rf"><- -> (rf)</option> | |
| 66 <option value="ff">-> -> (ff)</option> | |
| 67 </param> | |
| 68 <repeat name="files" title="Files"> | |
| 69 <conditional name="file_type"> | |
| 70 <param name="type" type="select" label="Select file format"> | |
| 71 <option value="separate">Separate input files</option> | |
| 72 <option value="interleaved">Interleaved files</option> | |
| 73 <option value="unpaired">Unpaired/Single reads</option> | |
| 74 </param> | |
| 75 <when value="separate"> | |
| 76 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> | |
| 77 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> | |
| 78 </when> | |
| 79 <when value="interleaved"> | |
| 80 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> | |
| 81 </when> | |
| 82 <when value="unpaired"> | |
| 83 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" /> | |
| 84 </when> | |
| 85 </conditional> | |
| 86 </repeat> | |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
87 </repeat> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
88 </inputs> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
89 <outputs> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
90 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
91 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
92 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
93 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
94 <data name="out_log" format="txt" label="SPAdes log" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
95 </outputs> |
| 2 | 96 <!-- <tests> |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
97 <test> |
| 2 | 98 |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
99 <param name="sc" value="false" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
100 <param name="careful" value="false" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
101 <param name="rectangle" value="false" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
102 <param name="threads" value="16" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
103 <param name="kmers" value="33,55" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
104 <param name="type" value="pairedend" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
105 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
106 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
107 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
108 </test> |
| 2 | 109 </tests> --> |
|
1
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
110 <help> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
111 **What it does** |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
112 |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
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. |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
114 |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
115 **Citation** |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
116 |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
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. |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
118 |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
119 </help> |
|
0f8b2da62d7d
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff
changeset
|
120 </tool> |