Mercurial > repos > jjohnson > gmap
diff gmap_build.xml @ 3:488e9d642566 draft
GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress
| author | peterjc |
|---|---|
| date | Wed, 28 Sep 2016 10:47:28 -0400 |
| parents | f6ba0f12cca2 |
| children | 14561eb803a5 |
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--- a/gmap_build.xml Wed Sep 28 10:43:44 2016 -0400 +++ b/gmap_build.xml Wed Sep 28 10:47:28 2016 -0400 @@ -1,121 +1,10 @@ -<tool id="gmap_build" name="GMAP Build" version="3.0.0"> +<tool id="gmap_build" name="GMAP Build" version="3.0.1"> <description>a database genome index for GMAP and GSNAP</description> <requirements> <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> - <version_string>gmap --version</version_string> + <version_command>gmap --version</version_command> <command interpreter="command"> /bin/bash $shscript > $output </command> - <inputs> - <!-- Name for this gmapdb --> - <param name="refname" type="text" label="Name you want to give this gmap database" help=""> - <validator type="empty_field" message="A database name is required."/> - </param> - <!-- Input data --> - <repeat name="inputs" title="Reference Sequence" min="1"> - <param name="input" type="data" format="fasta" label="reference sequence fasta" /> - </repeat> - - <param name="circular_chroms" type="text" value="" optional="true" label="Names of circular chromosomes" - help="a list of chromosomes, separated by commas, allow GSNAP and GMAP to align reads across the ends of the chromosome"> - </param> - - <param name="sort" type="select" label="Sort chromosomes" help=""> - <option value="none">none - use chromosomes as found in FASTA file(s)</option> - <option value="alpha">alpha - sort chromosomes alphabetically (chr10 before chr 1)</option> - <option value="numeric-alpha">numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY</option> - <option value="chrom">chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU</option> - </param> - - <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/> - <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/> - <conditional name="splicesite"> - <param name="splice_source" type="select" label="Add splice and intron info from" > - <option value="none"></option> - <option value="refGeneTable">refGenes table from UCSC table browser</option> - <option value="gtf">GTF</option> - <option value="gff3">GFF3</option> - </param> - <when value="none"/> - <when value="refGeneTable"> - <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" /> - <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" - help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> - <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> - </param> - - </when> - <when value="gtf"> - <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" /> - </when> - <when value="gff3"> - <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" /> - </when> - </conditional> - <conditional name="dbsnp"> - <param name="snp_source" type="select" label="Add SNP info from" > - <option value="none"></option> - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</option> - <option value="vcfFile">VCF File</option> - </param> - <when value="none"/> - <when value="snpTable"> - <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" /> - <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" /> - <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> - <option value="1" selected="true">1 (High)</option> - <option value="2">2 (Medium)</option> - <option value="3">3 (All)</option> - </param> - </when> - <when value="snpFile"> - <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" - help="Format (3 columns): - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - <br>Each line must start with a > character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) - <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. - If the one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a probable error. - The N stands for any other allele." /> - </when> - <when value="vcfFile"> - <param name="snps" type="data" format="vcf" optional="true" label="VCF SNPs file" - help="Example: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz - The VCF file contains multiple versions of dbSNP, so if you want a - particular version, such as 135. The vcf_iit program tries to pick - a subset of SNPs that somewhat parallel - the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs - that have been validated (marked in the VCF file as "VLD") or have a - submitter link-out ("SLO"). Otherwise, it excludes SNPs that are - individual genotypes ("GNO"). If none of these conditions hold, then - the SNP is allowed. "/> - <param name="vcf_version" type="text" value="" optional="true" label="dbSNP version" - help="The VCF file contains multiple versions of dbSNP, so if you want a particular version, such as 135"/> - </when> - </conditional> - - <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"> - <option value="12">12 (64MB RAM)</option> - <option value="13">13 (256MB RAM)</option> - <option value="14">14 (1GB RAM)</option> - <option value="15" selected="true">15 (4GB RAM)</option> - </param> - - </inputs> - <stdio> - <exit_code range="1" level="fatal" description="Error running gmap_build" /> - </stdio> - <outputs> - <!-- - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - --> - <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" /> - </outputs> <configfiles> <configfile name="shscript"> #!/bin/bash @@ -145,8 +34,8 @@ #else: gmap_build -D $gmapdb -d $refname -s $sort $circular #for i in $inputs# ${i.input}#end for# #end if -get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /' -echo "kmers: " $kmer +get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /' +echo "kmers: " $kmer #if $splicesite.splice_source == 'refGeneTable': #if $splicesite.refGenes.__str__ != 'None': cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'splicesites') @@ -190,15 +79,122 @@ atoiindex -d $refname echo "atoiindex" -d $refname #end if -get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' +get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' </configfile> </configfiles> + <inputs> + <!-- Name for this gmapdb --> + <param name="refname" type="text" label="Name you want to give this gmap database" help=""> + <validator type="empty_field" message="A database name is required."/> + </param> + <!-- Input data --> + <repeat name="inputs" title="Reference Sequence" min="1"> + <param name="input" type="data" format="fasta" label="reference sequence fasta" /> + </repeat> + <param name="circular_chroms" type="text" value="" optional="true" label="Names of circular chromosomes" + help="a list of chromosomes, separated by commas, allow GSNAP and GMAP to align reads across the ends of the chromosome"> + </param> + + <param name="sort" type="select" label="Sort chromosomes" help=""> + <option value="none">none - use chromosomes as found in FASTA file(s)</option> + <option value="alpha">alpha - sort chromosomes alphabetically (chr10 before chr 1)</option> + <option value="numeric-alpha">numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY</option> + <option value="chrom">chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU</option> + </param> + + <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/> + <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/> + <conditional name="splicesite"> + <param name="splice_source" type="select" label="Add splice and intron info from" > + <option value="none"></option> + <option value="refGeneTable">refGenes table from UCSC table browser</option> + <option value="gtf">GTF</option> + <option value="gff3">GFF3</option> + </param> + <when value="none"/> + <when value="refGeneTable"> + <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" /> + <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" + help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> + <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> + </param> + + </when> + <when value="gtf"> + <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" /> + </when> + <when value="gff3"> + <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" /> + </when> + </conditional> + <conditional name="dbsnp"> + <param name="snp_source" type="select" label="Add SNP info from" > + <option value="none"></option> + <option value="snpTable">UCSC SNP Table</option> + <option value="snpFile">GMAP SNP File</option> + <option value="vcfFile">VCF File</option> + </param> + <when value="none"/> + <when value="snpTable"> + <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" /> + <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" /> + <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> + <option value="1" selected="true">1 (High)</option> + <option value="2">2 (Medium)</option> + <option value="3">3 (All)</option> + </param> + </when> + <when value="snpFile"> + <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" + help="Format (3 columns): + <br>>rs62211261 21:14379270 CG + <br>>rs62211262 21:14379281 CG + <br>Each line must start with a > character, then be followed by an + identifier (which may have duplicates). Then there should be the + chromosomal coordinate of the SNP. (Coordinates are all 1-based, so + the first character of a chromosome is number 1.) Finally, there + should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) + <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. + If the one of these two letters does not match the allele in the reference + sequence, that SNP will be ignored in subsequent processing as a probable error. + The N stands for any other allele." /> + </when> + <when value="vcfFile"> + <param name="snps" type="data" format="vcf" optional="true" label="VCF SNPs file" + help="Example: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz + The VCF file contains multiple versions of dbSNP, so if you want a + particular version, such as 135. The vcf_iit program tries to pick + a subset of SNPs that somewhat parallel + the ones without exceptions in the UCSC dbSNP file. It keeps all SNPs + that have been validated (marked in the VCF file as "VLD") or have a + submitter link-out ("SLO"). Otherwise, it excludes SNPs that are + individual genotypes ("GNO"). If none of these conditions hold, then + the SNP is allowed. "/> + <param name="vcf_version" type="text" value="" optional="true" label="dbSNP version" + help="The VCF file contains multiple versions of dbSNP, so if you want a particular version, such as 135"/> + </when> + </conditional> + + <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"> + <option value="12">12 (64MB RAM)</option> + <option value="13">13 (256MB RAM)</option> + <option value="14">14 (1GB RAM)</option> + <option value="15" selected="true">15 (4GB RAM)</option> + </param> + </inputs> + <stdio> + <exit_code range="1" level="fatal" description="Error running gmap_build" /> + </stdio> + <outputs> + <!-- + <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> + --> + <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" /> + </outputs> <tests> - </tests> - + </tests> <help> - **GMAP Build** 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.) @@ -225,7 +221,7 @@ **Detecting known and novel splice sites in GSNAP** -GSNAP can detect splice junctions in individual reads. +GSNAP can detect splice junctions in individual reads. GSNAP allows for known splicing at two levels: at the level of known splice sites and at the level of known introns. At the site level, GSNAP finds splicing between arbitrary combinations of donor and @@ -237,8 +233,8 @@ than known introns, unless you are certain that all alternative splicing events are known are represented in your file. -Splice site files can be generated from a GTF file -or from refGenes table from UCSC. +Splice site files can be generated from a GTF file +or from refGenes table from UCSC. **SNP-tolerant alignment in GSNAP** @@ -285,7 +281,7 @@ GSNAP has the ability to align reads from bisulfite-treated DNA, which converts unmethylated cytosines to uracils that appear as thymines in -reads. GSNAP is able to identify genomic-T to read-C mismatches, +reads. GSNAP is able to identify genomic-T to read-C mismatches, if a cmetindex is generated. **RNA-editing tolerance in GSNAP** @@ -335,7 +331,8 @@ will overwrite only the identical files from the previous runs. You can then choose the k-mer size at run-time by using the -k flag for either GMAP or GSNAP. - </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bti310</citation> + </citations> </tool> -