| Previous changeset 4:4a53b89fa703 (2021-01-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 87fc41195cd9d05d431e8363c31898ce07369ed3" |
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modified:
velvetoptimiser.xml |
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| diff -r 4a53b89fa703 -r 82398ba86ba7 velvetoptimiser.xml --- a/velvetoptimiser.xml Wed Jan 13 15:31:18 2021 +0000 +++ b/velvetoptimiser.xml Sat Nov 27 10:38:38 2021 +0000 |
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| b'@@ -1,5 +1,8 @@\n-<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy1">\n+<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy2">\n <description>Automatically optimize Velvet assemblies</description>\n+ <xrefs>\n+ <xref type="bio.tools">velvetoptimiser</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="1.2.10">velvet</requirement>\n <requirement type="package" version="2.2.6">perl-velvetoptimiser</requirement>\n@@ -15,6 +18,7 @@\n -t "\\${GALAXY_SLOTS:-1}"\n -s $start_kmer\n -e $end_kmer\n+ -x $kmer_step\n -d out\n -f "\n #for $i in $files:\n@@ -61,22 +65,26 @@\n #end for\n "\n \n- ##if str($advanced.advanced_select) == "advanced"\n- $advanced.verbose\n- -k \'$advanced.optFuncKmer\'\n- -c \'$advanced.optFuncCov\'\n- #if str($advanced.velvetg_opts) != ""\n- -o \'$advanced.velvetg_opts\'\n- #end if\n- -m $advanced.minCutoff\n- -z $advanced.maxCutoff\n- ##end if\n+ $advanced.verbose\n+ -k \'$advanced.optFuncKmer\'\n+ -c \'$advanced.optFuncCov\'\n+ #if str($advanced.velvetg_opts) != ""\n+ -o \'$advanced.velvetg_opts\'\n+ #end if\n+ -m $advanced.minCutoff\n+ -z $advanced.maxCutoff\n \n ]]></command>\n <inputs>\n- <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" />\n- <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" />\n- <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" />\n+ <param name="start_kmer" argument="-s" type="integer" value="31" min="11" max="191" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value">\n+ <validator type="expression" message="Value needs to be odd">int(value) % 2 == 1</validator>\n+ </param>\n+ <param name="end_kmer" argument="-e" type="integer" value="191" min="11" max="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value">\n+ <validator type="expression" message="Value needs to be odd">int(value) % 2 == 1</validator>\n+ </param>\n+ <param name="kmer_step" argument="-x" type="integer" value="2" min="2" max="189" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range">\n+ <validator type="expression" message="Value needs to be even">int(value) % 2 == 0</validator>\n+ </param>\n \n <repeat name="files" title="Input files" min="1">\n <param name="filetype" label="Input file type" type="select" help="Input file type">\n@@ -108,12 +116,12 @@\n </repeat>\n \n <section name="advanced" title="Advanced Options" expanded="false">\n- <param name="verbose" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />\n- <param name="optFuncKmer" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>\n- <param name="optFuncCov" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>\n- <param name="velvetg_opts" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>\n- <param name="minCutoff" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverag'..b'on of the calculated expected coverage."/>\n+ <param name="verbose" argument="-v" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />\n+ <param name="optFuncKmer" argument="-k" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>\n+ <param name="optFuncCov" argument="-c" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>\n+ <param name="velvetg_opts" argument="-o" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>\n+ <param name="minCutoff" argument="-m" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverage cutoff to consider in the optimisation"/>\n+ <param name="maxCutoff" argument="-z" 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."/>\n </section>\n </inputs>\n \n@@ -236,10 +244,12 @@\n \n The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.\n \n- The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::\n- - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.\n- - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits\n- - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.\n+ The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints:\n+\n+ - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.\n+ - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits\n+ - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.\n+\n \n 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.\n 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.\n@@ -274,21 +284,15 @@\n Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate\n 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.\n \n- Supported file formats are::\n-\n- fasta\n- fastq\n- bam\n-\n- Read categories are::\n+ Supported file formats are: fasta, fastq, bam\n \n- short (default)\n- shortPaired\n- long (for Sanger, 454 or even reference sequences)\n- longPaired\n- reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)\n-\n-\n+ Read categories are: \n+ \n+ - short (default)\n+ - shortPaired\n+ - long (for Sanger, 454 or even reference sequences)\n+ - longPaired\n+ - reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)\n ]]></help>\n <citations>\n <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,\n' |