comparison gmap_build.xml @ 3:488e9d642566 draft

GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress

2:f6ba0f12cca2

<tool id="gmap_build" name="GMAP Build" version="3.0.0">
  <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>
  <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):
                &lt;br&gt;>rs62211261 21:14379270 CG
                &lt;br&gt;>rs62211262 21:14379281 CG
                &lt;br&gt;Each line must start with a &gt; 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)
                &lt;br&gt;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 &#34;VLD&#34;) or have a
                     submitter link-out (&#34;SLO&#34;).  Otherwise, it excludes SNPs that are
                     individual genotypes (&#34;GNO&#34;).  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
#set $ds = chr(36)
#set $gt = chr(62)

gmap_build -D $gmapdb -d $refname -s $sort $circular -k $k #for i in $inputs# ${i.input}#end for#
#end for
#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 
#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')
cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o  $os.path.join($mapsdir,'introns')
#end if

#end if
#if $atoiindex.__str__ == 'yes':
atoiindex -d $refname
echo "atoiindex" -d $refname
#end if
get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' 
    </configfile>
  </configfiles>

  <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.)

You will want to read the README_

genome in human beings is circular.


**Detecting known and novel splice sites in GSNAP**

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
acceptor splice sites, meaning that it can find alternative splicing
events.  At the intron level, GSNAP finds splicing only between the

alternative splicing events, only introns included in the given list.
For most purposes, I would recommend using known splice sites, rather
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.  


**SNP-tolerant alignment in GSNAP**

GSNAP has the ability to align to a reference space of all possible

**Alignment of reads from bisulfite-treated DNA in GSNAP**

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, 
if a cmetindex is generated.

**RNA-editing tolerance in GSNAP**

Just as GSNAP has a program cmetindex and a mode called "cmet" for

If you want to build your genomic databases with more than one k-mer
size, you can re-run gmap_build with different values of -k.  This
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>
</tool>

3:488e9d642566

<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_command>gmap --version</version_command>
  <command interpreter="command"> /bin/bash $shscript > $output </command>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash
#set $ds = chr(36)
#set $gt = chr(62)

gmap_build -D $gmapdb -d $refname -s $sort $circular -k $k #for i in $inputs# ${i.input}#end for#
#end for
#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
#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')
cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o  $os.path.join($mapsdir,'introns')
#end if

#end if
#if $atoiindex.__str__ == 'yes':
atoiindex -d $refname
echo "atoiindex" -d $refname
#end if
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):
                &lt;br&gt;>rs62211261 21:14379270 CG
                &lt;br&gt;>rs62211262 21:14379281 CG
                &lt;br&gt;Each line must start with a &gt; 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)
                &lt;br&gt;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 &#34;VLD&#34;) or have a
                     submitter link-out (&#34;SLO&#34;).  Otherwise, it excludes SNPs that are
                     individual genotypes (&#34;GNO&#34;).  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>
  <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.)

You will want to read the README_

genome in human beings is circular.


**Detecting known and novel splice sites in GSNAP**

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
acceptor splice sites, meaning that it can find alternative splicing
events.  At the intron level, GSNAP finds splicing only between the

alternative splicing events, only introns included in the given list.
For most purposes, I would recommend using known splice sites, rather
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.


**SNP-tolerant alignment in GSNAP**

GSNAP has the ability to align to a reference space of all possible

**Alignment of reads from bisulfite-treated DNA in GSNAP**

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,
if a cmetindex is generated.

**RNA-editing tolerance in GSNAP**

Just as GSNAP has a program cmetindex and a mode called "cmet" for

If you want to build your genomic databases with more than one k-mer
size, you can re-run gmap_build with different values of -k.  This
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>