gmap: gmap_build.xml annotate

annotate gmap_build.xml @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

author	peterjc
date	Fri, 21 Oct 2016 10:55:40 -0400
parents	488e9d642566
children

rev	line source
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	1 <tool id="gmap_build" name="GMAP Build" version="3.0.1">
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	2 <description>a database genome index for GMAP and GSNAP</description>
10e3476429b5 Uploaded jjohnson parents: diff changeset	3 <requirements>
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	4 <requirement type="package" version="2013-05-09">gmap</requirement>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	5 </requirements>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	6 <version_command>gmap --version</version_command>
5 14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	7 <command detect_errors="exit_code"><![CDATA[
14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	8 /bin/bash $shscript > $output
14561eb803a5 Uploaded v3.0.1b (still working on this prior to main Tool Shed release) peterjc parents: 3 diff changeset	9 ]]></command>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	10 <configfiles>
10e3476429b5 Uploaded jjohnson parents: diff changeset	11 <configfile name="shscript">
10e3476429b5 Uploaded jjohnson parents: diff changeset	12 #!/bin/bash
10e3476429b5 Uploaded jjohnson parents: diff changeset	13 #set $ds = chr(36)
10e3476429b5 Uploaded jjohnson parents: diff changeset	14 #set $gt = chr(62)
10e3476429b5 Uploaded jjohnson parents: diff changeset	15 #set $lt = chr(60)
10e3476429b5 Uploaded jjohnson parents: diff changeset	16 #set $ad = chr(38)
10e3476429b5 Uploaded jjohnson parents: diff changeset	17 ## #set $ref_files = ''
10e3476429b5 Uploaded jjohnson parents: diff changeset	18 ## #for $i in $inputs:
10e3476429b5 Uploaded jjohnson parents: diff changeset	19 ## #set $ref_files = $ref_files $i.input
10e3476429b5 Uploaded jjohnson parents: diff changeset	20 ## #end for
10e3476429b5 Uploaded jjohnson parents: diff changeset	21 ## echo $ref_files
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	22 #set circular = ""
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	23 #if $circular_chroms.__str__.strip() != '':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	24 #set circular = ('').join([' -c ','"', $circular_chroms.__str__,'"'])
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	25 #end if
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	26 #import os.path
10e3476429b5 Uploaded jjohnson parents: diff changeset	27 #set $gmapdb = $output.extra_files_path
10e3476429b5 Uploaded jjohnson parents: diff changeset	28 #set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps')
10e3476429b5 Uploaded jjohnson parents: diff changeset	29 mkdir -p $gmapdb
10e3476429b5 Uploaded jjohnson parents: diff changeset	30 ## export GMAPDB required for cmetindex and atoiindex
10e3476429b5 Uploaded jjohnson parents: diff changeset	31 export GMAPDB=$gmapdb
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	32 #if $kmer:
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	33 #for $k in $kmer.__str__.split(','):
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	34 gmap_build -D $gmapdb -d $refname -s $sort $circular -k $k #for i in $inputs# ${i.input}#end for#
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	35 #end for
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	36 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	37 gmap_build -D $gmapdb -d $refname -s $sort $circular #for i in $inputs# ${i.input}#end for#
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	38 #end if
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	39 get-genome -D $gmapdb -d '?' \| sed 's/^Available .*/gmap db: /'
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	40 echo "kmers: " $kmer
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	41 #if $splicesite.splice_source == 'refGeneTable':
10e3476429b5 Uploaded jjohnson parents: diff changeset	42 #if $splicesite.refGenes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	43 cat $splicesite.refGenes \| psl_splicesites -s $splicesite.col_skip \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	44 cat $splicesite.refGenes \| psl_introns -s $splicesite.col_skip \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	45 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	46 #elif $splicesite.splice_source == 'gtf':
10e3476429b5 Uploaded jjohnson parents: diff changeset	47 #if $splicesite.gtfGenes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	48 cat $splicesite.gtfGenes \| gtf_splicesites \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	49 cat $splicesite.gtfGenes \| gtf_introns \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	50 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	51 #elif $splicesite.splice_source == 'gff3':
10e3476429b5 Uploaded jjohnson parents: diff changeset	52 #if $splicesite.gff3Genes.__str__ != 'None':
10e3476429b5 Uploaded jjohnson parents: diff changeset	53 cat $splicesite.gff3Genes \| gff3_splicesites \| iit_store -o $os.path.join($mapsdir,'splicesites')
10e3476429b5 Uploaded jjohnson parents: diff changeset	54 cat $splicesite.gff3Genes \| gff3_introns \| iit_store -o $os.path.join($mapsdir,'introns')
10e3476429b5 Uploaded jjohnson parents: diff changeset	55 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	56 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	57 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	58 #if $dbsnp.snp_source == 'snpTable':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	59 #if $dbsnp.snpsex.__str__ != 'None':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	60 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	61 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	62 cat $dbsnp.snps \| dbsnp_iit -w $dbsnp.weight \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	63 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	64 #elif $dbsnp.snp_source == 'vcfFile':
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	65 #if $dbsnp.vcf_version and len($dbsnp.vcf_version.__str__.strip()) > 0:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	66 cat $dbsnp.snps \| vcf_iit -v $dbsnp.vcf_version.__str__.strip() \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	67 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	68 cat $dbsnp.snps \| vcf_iit \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	69 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	70 #else:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	71 cat $dbsnp.snps \| iit_store -o $os.path.join($mapsdir,'snps')
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	72 #end if
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	73 snpindex -d $refname -v snps
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	74 echo "snpindex" -d $refname -v snps
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	75 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	76 #if $cmetindex.__str__ == 'yes':
10e3476429b5 Uploaded jjohnson parents: diff changeset	77 cmetindex -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	78 echo "cmetindex" -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	79 #end if
10e3476429b5 Uploaded jjohnson parents: diff changeset	80 #if $atoiindex.__str__ == 'yes':
10e3476429b5 Uploaded jjohnson parents: diff changeset	81 atoiindex -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	82 echo "atoiindex" -d $refname
10e3476429b5 Uploaded jjohnson parents: diff changeset	83 #end if
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	84 get-genome -D $gmapdb -d $refname -m '?' \| sed 's/^Available maps .*/maps: /'
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	85 </configfile>
10e3476429b5 Uploaded jjohnson parents: diff changeset	86 </configfiles>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	87 <inputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	88 <!-- Name for this gmapdb -->
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	89 <param name="refname" type="text" label="Name you want to give this gmap database" help="">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	90 <validator type="empty_field" message="A database name is required."/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	91 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	92 <!-- Input data -->
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	93 <repeat name="inputs" title="Reference Sequence" min="1">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	94 <param name="input" type="data" format="fasta" label="reference sequence fasta" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	95 </repeat>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	96
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	97 <param name="circular_chroms" type="text" value="" optional="true" label="Names of circular chromosomes"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	98 help="a list of chromosomes, separated by commas, allow GSNAP and GMAP to align reads across the ends of the chromosome">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	99 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	100
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	101 <param name="sort" type="select" label="Sort chromosomes" help="">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	102 <option value="none">none - use chromosomes as found in FASTA file(s)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	103 <option value="alpha">alpha - sort chromosomes alphabetically (chr10 before chr 1)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	104 <option value="numeric-alpha">numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	105 <option value="chrom">chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	106 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	107
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	108 <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	109 <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	110 <conditional name="splicesite">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	111 <param name="splice_source" type="select" label="Add splice and intron info from" >
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	112 <option value="none"></option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	113 <option value="refGeneTable">refGenes table from UCSC table browser</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	114 <option value="gtf">GTF</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	115 <option value="gff3">GFF3</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	116 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	117 <when value="none"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	118 <when value="refGeneTable">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	119 <param name="refGenes" type="data" format="tabular" optional="true" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	120 <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	121 help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	122 <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	123 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	124
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	125 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	126 <when value="gtf">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	127 <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	128 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	129 <when value="gff3">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	130 <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	131 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	132 </conditional>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	133 <conditional name="dbsnp">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	134 <param name="snp_source" type="select" label="Add SNP info from" >
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	135 <option value="none"></option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	136 <option value="snpTable">UCSC SNP Table</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	137 <option value="snpFile">GMAP SNP File</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	138 <option value="vcfFile">VCF File</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	139 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	140 <when value="none"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	141 <when value="snpTable">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	142 <param name="snps" type="data" format="tabular" optional="true" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	143 <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	144 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	145 <option value="1" selected="true">1 (High)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	146 <option value="2">2 (Medium)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	147 <option value="3">3 (All)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	148 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	149 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	150 <when value="snpFile">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	151 <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	152 help="Format (3 columns):
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	153 <br>>rs62211261 21:14379270 CG
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	154 <br>>rs62211262 21:14379281 CG
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	155 <br>Each line must start with a > character, then be followed by an
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	156 identifier (which may have duplicates). Then there should be the
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	157 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	158 the first character of a chromosome is number 1.) Finally, there
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	159 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	160 <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome.
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	161 If the one of these two letters does not match the allele in the reference
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	162 sequence, that SNP will be ignored in subsequent processing as a probable error.
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	163 The N stands for any other allele." />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	164 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	165 <when value="vcfFile">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	166 <param name="snps" type="data" format="vcf" optional="true" label="VCF SNPs file"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	167 help="Example: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	168 The VCF file contains multiple versions of dbSNP, so if you want a
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	169 particular version, such as 135. The vcf_iit program tries to pick
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	170 a subset of SNPs that somewhat parallel
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	171 the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	172 that have been validated (marked in the VCF file as "VLD") or have a
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	173 submitter link-out ("SLO"). Otherwise, it excludes SNPs that are
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	174 individual genotypes ("GNO"). If none of these conditions hold, then
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	175 the SNP is allowed. "/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	176 <param name="vcf_version" type="text" value="" optional="true" label="dbSNP version"
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	177 help="The VCF file contains multiple versions of dbSNP, so if you want a particular version, such as 135"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	178 </when>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	179 </conditional>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	180
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	181 <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help="Use smaller values when building indexes on machines with limited RAM">
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	182 <option value="12">12 (64MB RAM)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	183 <option value="13">13 (256MB RAM)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	184 <option value="14">14 (1GB RAM)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	185 <option value="15" selected="true">15 (4GB RAM)</option>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	186 </param>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	187 </inputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	188 <outputs>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	189 <!--
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	190 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	191 -->
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	192 <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	193 </outputs>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	194 <tests>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	195 </tests>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	196 <help>
10e3476429b5 Uploaded jjohnson parents: diff changeset	197 GMAP Build
10e3476429b5 Uploaded jjohnson parents: diff changeset	198
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	199 GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). (GMAP Build uses GMAP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.)
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	200
10e3476429b5 Uploaded jjohnson parents: diff changeset	201 You will want to read the README_
10e3476429b5 Uploaded jjohnson parents: diff changeset	202
10e3476429b5 Uploaded jjohnson parents: diff changeset	203 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
10e3476429b5 Uploaded jjohnson parents: diff changeset	204
10e3476429b5 Uploaded jjohnson parents: diff changeset	205 .. _GMAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	206 .. _GSNAP: http://research-pub.gene.com/gmap/
10e3476429b5 Uploaded jjohnson parents: diff changeset	207 .. _README: http://research-pub.gene.com/gmap/src/README
10e3476429b5 Uploaded jjohnson parents: diff changeset	208 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
10e3476429b5 Uploaded jjohnson parents: diff changeset	209
10e3476429b5 Uploaded jjohnson parents: diff changeset	210
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	211 circular chromosomes
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	212
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	213 Finally, you can provide information to gmap_build that certain
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	214 chromosomes are circular, with the -c or -\-circular flag. The value
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	215 for these flags is a list of chromosomes, separated by commas. The
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	216 gmap_build program will then allow GSNAP and GMAP to align reads
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	217 across the ends of the chromosome. For example, the mitochondrial
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	218 genome in human beings is circular.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	219
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	220
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	221 Detecting known and novel splice sites in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	222
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	223 GSNAP can detect splice junctions in individual reads.
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	224 GSNAP allows for known splicing at two levels: at the level of known
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	225 splice sites and at the level of known introns. At the site level,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	226 GSNAP finds splicing between arbitrary combinations of donor and
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	227 acceptor splice sites, meaning that it can find alternative splicing
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	228 events. At the intron level, GSNAP finds splicing only between the
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	229 set of given donor-acceptor pairs, so it is constrained not to find
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	230 alternative splicing events, only introns included in the given list.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	231 For most purposes, I would recommend using known splice sites, rather
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	232 than known introns, unless you are certain that all alternative
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	233 splicing events are known are represented in your file.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	234
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	235 Splice site files can be generated from a GTF file
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	236 or from refGenes table from UCSC.
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	237
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	238
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	239 SNP-tolerant alignment in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	240
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	241 GSNAP has the ability to align to a reference space of all possible
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	242 major and minor alleles in a set of known SNPs provided by the user.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	243
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	244
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	245 Process known SNP data, either from older dbSNP files or from newer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	246 files in VCF format. The older dbSNP files can be obtained from UCSC,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	247 either from the Galaxy UCSC table browser or downloaded:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	248
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	249 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	250
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	251 For versions before snp132, you may also want to exclude exceptions,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	252 which will require this file:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	253
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	254 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	255
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	256 The option "-w weight" makes use of the dbSNP item weight, a value
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	257 from 1 to 3, where lower weight means higher confidence. Items will
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	258 be included if the item weight is the given value weight or less.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	259 The default value of -w is 1, which is the criterion UCSC uses to
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	260 build its ambiguous version of the genome. To allow all item weights,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	261 specify "-w 3".
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	262
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	263 The more recent SNP data are provided in VCF format, and can be
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	264 retrieved like this:
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	265
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	266 ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	267
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	268 The VCF file contains multiple versions of dbSNP, so if you want a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	269 particular version, such as 135, you would use the flag "-v 135". The
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	270 vcf_iit program tries to pick a subset of SNPs that somewhat parallel
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	271 the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	272 that have been validated (marked in the VCF file as "VLD") or have a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	273 submitter link-out ("SLO"). Otherwise, it excludes SNPs that are
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	274 individual genotypes ("GNO"). If none of these conditions hold, then
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	275 the SNP is allowed. These rules might not be the best ones; I made
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	276 them up by trying to compare version 135 of the VCF data with
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	277 version 135 of the UCSC dbSNP data.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	278
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	279 Alignment of reads from bisulfite-treated DNA in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	280
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	281 GSNAP has the ability to align reads from bisulfite-treated DNA, which
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	282 converts unmethylated cytosines to uracils that appear as thymines in
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	283 reads. GSNAP is able to identify genomic-T to read-C mismatches,
2 f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	284 if a cmetindex is generated.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	285
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	286 RNA-editing tolerance in GSNAP
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	287
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	288 Just as GSNAP has a program cmetindex and a mode called "cmet" for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	289 tolerance to C-to-T changes, it can be tolerant to A-to-G changes
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	290 using the program atoiindex and a mode called "atoi". This mode is
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	291 designed to facilitate alignments that are tolerant to RNA editing
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	292 where A's are converted to I's, which appear as G's to a sequencer.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	293
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	294 To process reads under RNA-editing tolerance, you will first need to
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	295 create th atoi index.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	296
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	297
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	298
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	299 K-mer size
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	300
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	301 You can control the k-mer size
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	302 for the genomic index with the -k flag, which can range from 12 to 15.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	303 The default value for -k is 15, but this requires your machine to have
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	304 4 GB of RAM to build the indices. If you do not have 4 GB of RAM,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	305 then you will need to reduce the value of -k or find another machine.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	306 Here are the RAM requirements for building various indices::
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	307
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	308 k-mer of 12: 64 MB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	309 k-mer of 13: 256 MB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	310 k-mer of 14: 1 GB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	311 k-mer of 15: 4 GB
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	312
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	313 These are the RAM requirements for building indices, but not to run
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	314 the GMAP/GSNAP programs once the indices are built, because the
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	315 genomic indices are compressed. For example, the genomic index for a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	316 k-mer of 15 gives a gammaptrs file of 64 MB and an offsetscomp file of
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	317 about 350 MB, much smaller than the 4 GB that would otherwise be
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	318 required. Therefore, you may want to build your genomic index on a
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	319 computer with sufficient RAM, and distribute that index to be used by
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	320 computers with less RAM.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	321
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	322 The amount of compression can be controlled using the -b or -\-basesize
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	323 parameter to gmap_build. By default, the value for k-mer size is 15,
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	324 and the value for basesize is 12. If you select a different value for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	325 k-mer size, then basesize is made by default to be equal to that k-mer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	326 size.
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	327
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	328 If you want to build your genomic databases with more than one k-mer
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	329 size, you can re-run gmap_build with different values of -k. This
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	330 will overwrite only the identical files from the previous runs. You
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	331 can then choose the k-mer size at run-time by using the -k flag for
f6ba0f12cca2 Untested work-in-progress GMAP wrappers v3.0.0, from JJ back in June 2013 peterjc parents: 1 diff changeset	332 either GMAP or GSNAP.
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	333 </help>
3 488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	334 <citations>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	335 <citation type="doi">10.1093/bioinformatics/bti310</citation>
488e9d642566 GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress peterjc parents: 2 diff changeset	336 </citations>
0 10e3476429b5 Uploaded jjohnson parents: diff changeset	337 </tool>

Mercurial > repos > jjohnson > gmap

annotate gmap_build.xml @ 5:14561eb803a5 draft