Mercurial > repos > crs4 > ssake
annotate ssake.xml @ 2:f20db7280f89 draft default tip
Fix SSAKE download URL (thanks to Graham Etherington for reporting this). Update Orione citation.
| author | crs4 |
|---|---|
| date | Thu, 06 Mar 2014 11:50:08 -0500 |
| parents | 386166019772 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ssake" name="SSAKE" version="0.0.10"> |
| 2 <description>short DNA sequences assembler</description> | |
| 3 <requirements> | |
| 1 | 4 <requirement type="package" version="3.8.1">ssake</requirement> |
| 0 | 5 </requirements> |
| 1 | 6 <version_command>SSAKE 2>&1 | sed -n 's/.*\(SSAKE \[.*\]\).*/\1/p'</version_command> |
| 0 | 7 <command interpreter="python"> |
| 8 ssake.py | |
| 9 #if $kind_of_reads.kind_of_reads_select == '0' | |
| 10 --if_unpaired $infile | |
| 11 #else | |
| 12 --if_paired_r1 $infile_r1 | |
| 13 --if_paired_r2 $infile_r2 | |
| 14 --iz ${kind_of_reads.insert_size} | |
| 15 -k ${kind_of_reads.minnumlinks} | |
| 16 -e ${kind_of_reads.error} | |
| 17 -a ${kind_of_reads.maxlinkratio} | |
| 18 -x ${kind_of_reads.minoverlap} | |
| 19 #end if | |
| 20 #if $seeds | |
| 21 -s $seeds | |
| 22 #end if | |
| 23 -w $mindepthofcoverage | |
| 24 -m $minoverlap | |
| 25 -o $mincall | |
| 26 -r $baseratio | |
| 27 --ignore_header 1 | |
| 28 --kind_of_reads ${kind_of_reads.kind_of_reads_select} | |
| 29 --out1 $contig | |
| 30 --out2 $short | |
| 31 --out3 $singlets | |
| 32 --logfile $log | |
| 33 </command> | |
| 34 <inputs> | |
| 35 <conditional name="kind_of_reads"> | |
| 36 <param name="kind_of_reads_select" type="select" label="Kind of reads (-p)"> | |
| 37 <option value="0">Unpaired </option> | |
| 38 <option value="1">Paired and equal (both files must have the same number of sequences, arranged in the same order)</option> | |
| 39 <option value="2">Paired and unequal (files can have different number of sequences in any order)</option> | |
| 40 </param> | |
| 41 <when value="0"> | |
| 42 <param name="infile" type="data" format="fasta" label="Input FASTA file" /> | |
| 43 </when> | |
| 44 <when value="1"> | |
| 45 <param name="infile_r1" type="data" format="fasta" label="Input FASTA file (read 1)" /> | |
| 46 <param name="infile_r2" type="data" format="fasta" label="Input FASTA file (read 2)" /> | |
| 47 <param name="insert_size" type="integer" value="200" label="Library insert size" /> | |
| 48 <param name="minnumlinks" type="integer" value="4" label="Minimum number of links (read pairs) to compute scaffold (-k)" /> | |
| 49 <param name="error" type="float" value="0.75" min="0" max="1" label="Error (%) allowed on mean distance (-e)" /> | |
| 50 <param name="maxlinkratio" type="float" value="0.5" label="Maximum link ratio between two best contig pairs (-a)" /> | |
| 51 <param name="minoverlap" type="integer" value="20" label="Minimum overlap required between contigs to merge adjacent contigs in a scaffold (-x)" /> | |
| 52 </when> | |
| 53 <when value="2"> | |
| 54 <param name="infile_r1" type="data" format="fasta" label="Input FASTA file (read 1)" /> | |
| 55 <param name="infile_r2" type="data" format="fasta" label="Input FASTA file (read 2)" /> | |
| 56 <param name="insert_size" type="integer" value="200" label="Library insert size" /> | |
| 57 <param name="minnumlinks" type="integer" value="4" label="Minimum number of links (read pairs) to compute scaffold (-k)" /> | |
| 58 <param name="error" type="float" value="0.75" min="0" max="1" label="Error (%) allowed on mean distance (-e)" /> | |
| 59 <param name="maxlinkratio" type="float" value="0.5" label="Maximum link ratio between two best contig pairs (-a)" /> | |
| 60 <param name="minoverlap" type="integer" value="20" label="Minimum overlap required between contigs to merge adjacent contigs in a scaffold (-x)" /> | |
| 61 </when> | |
| 62 </conditional> | |
| 63 <param name="seeds" type="data" format="fasta" optional="true" label="FASTA file containing sequences to use as seeds exclusively (-s)" help="Optional, specify only if different from read set" /> | |
| 64 <param name="mindepthofcoverage" type="integer" value="1" label="Minimum depth of coverage allowed for contigs (-w)" /> | |
| 65 <param name="minoverlap" type="integer" value="20" label="Minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m)" /> | |
| 66 <param name="mincall" type="integer" value="2" label="Minimum number of reads needed to call a base during an extension (-o)" /> | |
| 67 <param name="baseratio" type="float" value="0.7" label="Minimum base ratio used to accept a overhang consensus base (-r)" /> | |
| 68 </inputs> | |
| 69 | |
| 70 <outputs> | |
| 71 <data name="contig" format="fasta" label="${tool.name} on ${on_string}: contigs" /> | |
| 72 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" /> | |
| 73 <data name="short" format="txt" label="${tool.name} on ${on_string}: unacceptable reads" /> | |
| 74 <data name="singlets" format="fasta" label="${tool.name} on ${on_string}: unassembled reads" /> | |
| 75 </outputs> | |
| 76 <help> | |
| 77 **What it does** | |
| 78 | |
| 79 SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. | |
| 80 It is an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd. | |
| 81 | |
| 82 **License and citation** | |
| 83 | |
| 84 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_. | |
| 85 | |
| 86 .. _CRS4 Srl.: http://www.crs4.it/ | |
| 87 .. _MIT license: http://opensource.org/licenses/MIT | |
| 88 | |
| 89 If you use this tool in Galaxy, please cite |Cuccuru2013|_. | |
| 90 | |
|
2
f20db7280f89
Fix SSAKE download URL (thanks to Graham Etherington for reporting this). Update Orione citation.
crs4
parents:
1
diff
changeset
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91 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted |
| 0 | 92 .. _Cuccuru2013: http://orione.crs4.it/ |
| 93 | |
| 94 This tool uses `SSAKE`_, which is licensed separately. Please cite |Warren2007|_. | |
| 95 | |
| 96 .. _SSAKE: http://www.bcgsc.ca/platform/bioinfo/software/ssake/ | |
| 97 .. |Warren2007| replace:: Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500-501 | |
| 98 .. _Warren2007: http://bioinformatics.oxfordjournals.org/content/23/4/500 | |
| 99 </help> | |
| 100 </tool> |