Mercurial > repos > crs4 > ssake
view 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 |
line wrap: on
line source
<tool id="ssake" name="SSAKE" version="0.0.10"> <description>short DNA sequences assembler</description> <requirements> <requirement type="package" version="3.8.1">ssake</requirement> </requirements> <version_command>SSAKE 2>&1 | sed -n 's/.*\(SSAKE \[.*\]\).*/\1/p'</version_command> <command interpreter="python"> ssake.py #if $kind_of_reads.kind_of_reads_select == '0' --if_unpaired $infile #else --if_paired_r1 $infile_r1 --if_paired_r2 $infile_r2 --iz ${kind_of_reads.insert_size} -k ${kind_of_reads.minnumlinks} -e ${kind_of_reads.error} -a ${kind_of_reads.maxlinkratio} -x ${kind_of_reads.minoverlap} #end if #if $seeds -s $seeds #end if -w $mindepthofcoverage -m $minoverlap -o $mincall -r $baseratio --ignore_header 1 --kind_of_reads ${kind_of_reads.kind_of_reads_select} --out1 $contig --out2 $short --out3 $singlets --logfile $log </command> <inputs> <conditional name="kind_of_reads"> <param name="kind_of_reads_select" type="select" label="Kind of reads (-p)"> <option value="0">Unpaired </option> <option value="1">Paired and equal (both files must have the same number of sequences, arranged in the same order)</option> <option value="2">Paired and unequal (files can have different number of sequences in any order)</option> </param> <when value="0"> <param name="infile" type="data" format="fasta" label="Input FASTA file" /> </when> <when value="1"> <param name="infile_r1" type="data" format="fasta" label="Input FASTA file (read 1)" /> <param name="infile_r2" type="data" format="fasta" label="Input FASTA file (read 2)" /> <param name="insert_size" type="integer" value="200" label="Library insert size" /> <param name="minnumlinks" type="integer" value="4" label="Minimum number of links (read pairs) to compute scaffold (-k)" /> <param name="error" type="float" value="0.75" min="0" max="1" label="Error (%) allowed on mean distance (-e)" /> <param name="maxlinkratio" type="float" value="0.5" label="Maximum link ratio between two best contig pairs (-a)" /> <param name="minoverlap" type="integer" value="20" label="Minimum overlap required between contigs to merge adjacent contigs in a scaffold (-x)" /> </when> <when value="2"> <param name="infile_r1" type="data" format="fasta" label="Input FASTA file (read 1)" /> <param name="infile_r2" type="data" format="fasta" label="Input FASTA file (read 2)" /> <param name="insert_size" type="integer" value="200" label="Library insert size" /> <param name="minnumlinks" type="integer" value="4" label="Minimum number of links (read pairs) to compute scaffold (-k)" /> <param name="error" type="float" value="0.75" min="0" max="1" label="Error (%) allowed on mean distance (-e)" /> <param name="maxlinkratio" type="float" value="0.5" label="Maximum link ratio between two best contig pairs (-a)" /> <param name="minoverlap" type="integer" value="20" label="Minimum overlap required between contigs to merge adjacent contigs in a scaffold (-x)" /> </when> </conditional> <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" /> <param name="mindepthofcoverage" type="integer" value="1" label="Minimum depth of coverage allowed for contigs (-w)" /> <param name="minoverlap" type="integer" value="20" label="Minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m)" /> <param name="mincall" type="integer" value="2" label="Minimum number of reads needed to call a base during an extension (-o)" /> <param name="baseratio" type="float" value="0.7" label="Minimum base ratio used to accept a overhang consensus base (-r)" /> </inputs> <outputs> <data name="contig" format="fasta" label="${tool.name} on ${on_string}: contigs" /> <data name="log" format="txt" label="${tool.name} on ${on_string}: log" /> <data name="short" format="txt" label="${tool.name} on ${on_string}: unacceptable reads" /> <data name="singlets" format="fasta" label="${tool.name} on ${on_string}: unassembled reads" /> </outputs> <help> **What it does** SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. It is an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd. **License and citation** This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT If you use this tool in Galaxy, please cite |Cuccuru2013|_. .. |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 .. _Cuccuru2013: http://orione.crs4.it/ This tool uses `SSAKE`_, which is licensed separately. Please cite |Warren2007|_. .. _SSAKE: http://www.bcgsc.ca/platform/bioinfo/software/ssake/ .. |Warren2007| replace:: Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500-501 .. _Warren2007: http://bioinformatics.oxfordjournals.org/content/23/4/500 </help> </tool>