Mercurial > repos > crs4 > ssake
diff ssake.xml @ 0:0ec408bcfc80 draft
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author | crs4 |
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date | Wed, 11 Sep 2013 12:51:21 -0400 |
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children | 386166019772 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ssake.xml Wed Sep 11 12:51:21 2013 -0400 @@ -0,0 +1,99 @@ +<tool id="ssake" name="SSAKE" version="0.0.10"> + <description>short DNA sequences assembler</description> + <requirements> + <requirement type="package" version="3.8">ssake</requirement> + </requirements> + <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. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* +.. _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>