velvetoptimiser: velvetoptimiser.xml annotate

annotate velvetoptimiser.xml @ 3:37d88f41c810 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

author	iuc
date	Tue, 30 Oct 2018 20:29:42 -0400
parents	0e2b4e3f9ca1
children	4a53b89fa703

rev	line source
3 37d88f41c810 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 2 diff changeset	1 <tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6">
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	2 <description>Automatically optimize Velvet assemblies</description>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	3 <requirements>
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	4 <requirement type="package" version="1.2.10">velvet</requirement>
3 37d88f41c810 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 2 diff changeset	5 <requirement type="package" version="2.2.6">perl-velvetoptimiser</requirement>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	6 </requirements>
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	7 <version_command>VelvetOptimiser.pl --version</version_command>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	8 <command detect_errors="exit_code"><![CDATA[
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	9 export OMP_NUM_THREADS=2 &&
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	10 export OMP_THREAD_LIMIT=2 &&
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	11 VelvetOptimiser.pl
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	12 -t "\${GALAXY_SLOTS:-1}"
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	13 -s $start_kmer
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	14 -e $end_kmer
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	15 -d out
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	16 -f "
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	17 #for $i in $files:
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	18 -${i.filetype}
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	19
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	20 #if str($i.paired_type.paired_type_selector) == "paired":
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	21
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	22 #if $i.__index__ > 1:
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	23 -shortPaired$i.__index__
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	24 #else
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	25 -shortPaired
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	26 #end if
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	27
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	28 -separate '$i.paired_type.input1' '$i.paired_type.input2'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	29 #end if
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	30
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	31 #if str($i.paired_type.paired_type_selector) == "single"
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	32
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	33 #if $i.__index__ > 1
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	34 -short$i.__index__
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	35 #else
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	36 -short
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	37 #end if
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	38
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	39 '$i.paired_type.input1'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	40 #end if
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	41
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	42 #if str($i.paired_type.paired_type_selector) == "paired_collection"
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	43 #if $i.__index__ > 1
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	44 -shortPaired$i.__index__
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	45 #else
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	46 -shortPaired
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	47 #end if
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	48 -separate '$i.paired_type.input1.forward' '$i.paired_type.input1.reverse'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	49 #end if
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	50 #if str($i.paired_type.paired_type_selector) == "paired_iv"
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	51 #if $i.__index__ > 1
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	52 -shortPaired$i.__index__
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	53 #else
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	54 -shortPaired
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	55 #end if
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	56 '$i.paired_type.input1'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	57 #end if
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	58 #end for
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	59 "
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	60
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	61 ##if str($advanced.advanced_select) == "advanced"
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	62 $advanced.verbose
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	63 -k '$advanced.optFuncKmer'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	64 -c '$advanced.optFuncCov'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	65 #if str($advanced.velvetg_opts) != ""
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	66 -o '$advanced.velvetg_opts'
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	67 #end if
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	68 -m $advanced.minCutoff
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	69 -z $advanced.maxCutoff
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	70 ##end if
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	71
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	72 ]]></command>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	73 <inputs>
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	74 <param name="start_kmer" type="integer" value="31" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	75 <param name="end_kmer" type="integer" value="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	76 <param name="kmer_step" type="integer" value="2" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range" />
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	77
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	78 <repeat name="files" title="Input files" min="1">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	79 <param name="filetype" label="Input file type" type="select" help="Input file type">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	80 <option value="fastq">Fastq</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	81 <option value="fasta">Fasta</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	82 <option value="bam">Bam</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	83 </param>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	84 <conditional name="paired_type">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	85 <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	86 <option value="paired">Paired</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	87 <option value="single">Single</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	88 <option value="paired_collection">Paired Collection</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	89 <option value="paired_iv">Paired Interleaved</option>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	90 </param>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	91 <when value="paired">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	92 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	93 <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	94 </when>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	95 <when value="single">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	96 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	97 </when>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	98 <when value="paired_collection">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	99 <param name="input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	100 </when>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	101 <when value="paired_iv">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	102 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select set of interleaved reads" help="Specify dataset with interleaved paired reads"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	103 </when>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	104 </conditional>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	105 </repeat>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	106
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	107 <section name="advanced" title="Advanced Options" expanded="false">
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	108 <param name="verbose" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	109 <param name="optFuncKmer" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	110 <param name="optFuncCov" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	111 <param name="velvetg_opts" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	112 <param name="minCutoff" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverage cutoff to consider in the optimisation"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	113 <param name="maxCutoff" type="float" value="0.8" label="Maximum coverage cutoff" help="The maximum coverage cutoff to consider expressed as a fraction of the calculated expected coverage."/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	114 </section>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	115 </inputs>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	116
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	117 <outputs>
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	118 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	119 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Contig Stats" from_work_dir="out/stats.txt"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	120 <data format="tabular" name="logfile" label="${tool.name} on ${on_string}: Log file" hidden="true" from_work_dir="*_Logfile.txt"/>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	121 </outputs>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	122
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	123 <tests>
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	124 <test>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	125 <param name="start_kmer" value="21" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	126 <param name="end_kmer" value="31" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	127 <param name="files_0\|filetype" value="fasta" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	128 <param name="files_0\|paired_type\|paired_type_selector" value="single" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	129 <param name="files_0\|paired_type\|input1" value="test_reads.fa" ftype="fasta" />
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	130 <output name="contigs" ftype="fasta" file="test-contigs.fa" compare="sim_size"/>
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	131 </test>
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	132 </tests>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	133
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	134 <help><![CDATA[
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	135 Velvet Optimiser Overview
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	136
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	137 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	138
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	139 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	140
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	141 Read the Velvet `documentation`__ for details on using the Vevlet Assembler.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	142
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	143 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	144
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	145 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	146
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	147 VelvetOptimiser
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	148
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	149 VelvetOptimiser_ was written by Simon Gladman of CSIRO/Melbourne University.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	150
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	151 VelvetOptimiser performs a number of velveth and velvetg steps to try and optimise an assembly based on the metrics provided below.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	152
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	153 .. _VelvetOptimiser: http://github.com/Slugger70/VelvetOptimiser
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	154
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	155 Galaxy tool wrapper for newer versions (2.5.5) of Velvet Optimiser. Written by Simon Gladman of Melbourne University.
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	156
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	157 Outputs
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	158
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	159
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	160 Contigs
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	161
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	162 The contigs.fa file.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	163 This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig lgth threshold, then the contigs shorter than that value are omitted.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	164 Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	165 The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	166
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	167 Stats
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	168
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	169 The stats.txt file.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	170 This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	171 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	172 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	173 Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	174
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	175 LastGraph
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	176
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	177 The LastGraph file.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	178 This file describes in its entirety the graph produced by Velvet. This file is hidden by default.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	179
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	180 Logfile
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	181
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	182 The Velvet Optimiser's logfile. This file is hidden by default
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	183
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	184 STDERR
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	185
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	186 The Standard Error output of the Optimiser for error messages etc. This file is hidden by default.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	187
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	188 Advanced options
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	189
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	190 Verbose : Include verbose velvet output in log file. Good for debugging when things don't work.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	191
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	192 Other Velvetg Options : Extra velvetg options to pass through. eg. -long_mult_cutoff -max_coverage etc (default '') See below for details.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	193
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	194 Minimum coverage cutoff : The minimum cov_cutoff to be used. (default '0').
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	195
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	196 Maximum coverage cutoff : The maximum coverage cutoff to consider as a multiplier of the expected coverage. (default '0.8').
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	197
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	198 K-mer optimisation function : The optimisation function used for k-mer choice. (default 'n50').
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	199
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	200 Coverage cutoff optimisation function : The optimisation function used for cov_cutoff optimisation. (default 'Lbp').
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	201
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	202 Velvet optimiser assembly optimisation functions can be built from the following variables.
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	203
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	204 LNbp = The total number of Ns in large contigs
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	205
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	206 Lbp = The total number of base pairs in large contigs
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	207
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	208 Lcon = The number of large contigs
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	209
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	210 max = The length of the longest contig
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	211
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	212 n50 = The n50
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	213
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	214 ncon = The total number of contigs
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	215
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	216 tbp = The total number of basepairs in contigs
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	217
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	218 Examples are:
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	219
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	220 'Lbp' = Just the total basepairs in contigs longer than 1kb
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	221
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	222 'n50*Lcon' = The n50 times the number of long contigs.
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	223
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	224 'n50*Lcon/tbp+log(Lbp)' = The n50 times the number of long contigs divided by the total bases in all contigs plus the log of the number of bases in long contigs (as an example only.)
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	225
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	226 Defaults are:
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	227
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	228 n50 for k-mer length optimisation &
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	229
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	230 Lbp for coverage cutoff
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	231
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	232 Hash Length
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	233
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	234 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	235
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	236 The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	237 - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	238 - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	239 - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	240
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	241 Now you still have quite a lot of possibilities. As is often the case, it's a trade-off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below)... so there's a sweet spot to be found with time and experience.
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	242 We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C * (L - k + 1)/L where k is your hash length, and L you read length.
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	243 Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	244
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	245
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	246 Velvetg options
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	247
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	248 -scaffolding yes\|no : scaffolding of contigs used paired end information (default: on)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	249
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	250 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	251
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	252 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	253
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	254 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	255
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	256 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	257
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	258 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	259
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	260 -coverage_mask integer : minimum coverage required for confident regions of contigs (default: 1)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	261
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	262 -long_mult_cutoff integer : minimum number of long reads required to merge contigs (default: 2)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	263
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	264 -paired_exp_fraction double : remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	265
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	266 -conserveLong yes\|no : preserve sequences with long reads in them (default no)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	267
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	268
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	269 Input Files
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	270
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	271 Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	272 read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	273
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	274 Supported file formats are::
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	275
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	276 fasta
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	277 fastq
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	278 bam
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	279
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	280 Read categories are::
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	281
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	282 short (default)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	283 shortPaired
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	284 long (for Sanger, 454 or even reference sequences)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	285 longPaired
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	286 reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	287
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	288
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	289 ]]></help>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	290 <citations>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	291 <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,
1 7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	292 author = "Gladman Simon",
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	293 title = "VelvetOptimiser",
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	294 year = "2012",
7db5615f4621 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae iuc parents: 0 diff changeset	295 note = "https://github.com/slugger70/VelvetOptimiser"}
0 d81360ea69d8 Initial upload simon-gladman parents: diff changeset	296 </citation>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	297 <citation type="doi">10.1101/gr.074492.107</citation>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	298 <citation type="doi">10.1371/journal.pone.0008407</citation>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	299 </citations>
d81360ea69d8 Initial upload simon-gladman parents: diff changeset	300 </tool>

Mercurial > repos > simon-gladman > velvetoptimiser

annotate velvetoptimiser.xml @ 3:37d88f41c810 draft