varextract.xml

<tool id="mimodd_varextract" name="MiModD Extract Variant Sites" 
version="@MIMODD_WRAPPER_VERSION@">
    <description>from a BCF file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
	mimodd varextract '$ifile'
	  #if $len($sitesinfo)
	    -p
	    #for $source in $sitesinfo
          '${source.pre_vcf}'
	    #end for
	  #end if
	  --ofile '$output_vcf'
	  $keep_alts
	  --verbose
    ]]></command>

    <inputs>
        <param name="ifile" type="data" format="bcf" label="BCF input file"
        help="Use the MiModD Variant Calling tool to generate the input for this tool."/>
        <repeat name="sitesinfo" title="include information from pre-calculated vcf dataset" default="0">
	        <param name="pre_vcf" type="data" format="vcf"
	        label="independently generated vcf datset" />
        </repeat>
        <param name="keep_alts" type="boolean" truevalue="-a" falsevalue="" checked="false"
        label="keep all sites with alternate bases"
        help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." />
    </inputs>
    <outputs>
        <data name="output_vcf" format="vcf"
        label="Variants extracted with MiModd from ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="ifile" value="a.bcf" />
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.N2.ot266" />
                </assert_contents>
            </output>
            <assert_command>
                <not_has_text text="-a" />
            </assert_command>
        </test>
        <test>
            <param name="ifile" value="a_part2.bcf" />
            <param name="keep_alts" value="true" />
            <param name="pre_vcf" value="a.vcf" />
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.ot266.external_source_1_N2.external_source_1_ot266" />
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="-a" />
            </assert_command>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

   **What it does**

The tool takes as input a BCF dataset like the ones produced by the
*MiModD Variant Calling* tool, extracts just the variant sites from it and
reports them in VCF format.

If the BCF input file specifies multiple samples, sites are included if they qualify as variant sites in at least one sample.

----------

**Options:**

**keep all sites with alternate bases**

By default, a variant site is considered to be a position in the genome for
which a non-reference allele appears in the inferred genotype of any sample. 

You can select the *keep all sites with alternate bases* option, if instead
you want to extract all sites, for which at least one non-reference base has
been observed (whether resulting in a non-reference allele call or not).
Using this option should rarely be necessary, but could be occassionally
helpful for closer inspection of candidate genomic regions.

 
**include information from pre-calculated vcf dataset**

During the process of variant extraction the tool can take into account
genome positions specified in one or more independently generated VCF datasets.
If such additional VCF input is provided, the tool output will contain the
samples found in these files as additional samples and sites from the main BCF
dataset will be included not only if they qualify as variant sites in at least
one sample specified in the BCF, but also if they are listed in any of the
additional VCF datasets.

Optional VCF input can be particularly useful in one of the following
situations:
   
1) you have prior information that leads you to think that certain genome
   positions are of special relevance for your project and, thus, you are
   interested in the statistics produced by the variant caller for these
   positions even if they are not considered variant sites. In this case you
   can use a minimal VCF dataset to guide the variant extraction process to
   include these positions. This dataset needs a minimal header of the form:

   ``##fileformat=VCFv4.2``

   followed by positional information like in this example::
 						     
     #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
     chrI	1222	.	.	.	.	.	.
     chrI	2651	.	.	.	.	.	.
     chrI	3659	.	.	.	.	.	.
     chrI	3731	.	.	.	.	.	.
  
   , where columns are tab-separated and . serves as a placeholder for missing
   information.
  
2) you have actual variant calls from an additional sample, but you do not
   have access to the original sequenced reads data (if you had, the
   recommended approach would be to include that data in the
   *MiModD Variant Calling* step. 

   This situation is often encountered with published datasets. Assume you
   have obtained a list of known single nucleotide variants (SNVs) found in
   one particular strain of your favorite model organism and you would like
   to know which of these SNVs are present in the related strains you have
   sequenced. You have aligned the sequenced reads from your samples and have
   used the *MiModD Variant Calling* tool, which has generated a BCF dataset
   ready for variant extraction. If the SNV list for the previously sequenced
   strain is in VCF format already, you can now just plug it into the
   analysis process by specifying it in the tool interface as an
   *independently generated vcf dataset*.
   The resulting vcf output will contain all SNV sites along with the variant
   sites found in the BCF alone. You can then proceed to the
   *MiModD VCF Filter* tool to look at the original SNV sites only or to
   investigate any other interesting subset of sites. If the SNV list is in
   some other format, you will have o convert it to VCF first. At a minimum,
   the dataset must have a ``##fileformat`` header line like the previous
   example and have the ``REF`` and ``ALT`` column filled in like so::

     #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
     chrI	1897409	.	A	G	.	.	.
     chrI	1897492	.	C	T	.	.	.
     chrI	1897616	.	C	A	.	.	.
     chrI	1897987	.	A	T	.	.	.
     chrI	1898185	.	C	T	.	.	.
     chrI	1898715	.	G	A	.	.	.
     chrI	1898729	.	T	C	.	.	.
     chrI	1900288	.	T	A	.	.	.
  
   , in which case the tool will assume that the corresponding sample is
   homozygous for each of the SNVs.
   If you need to distinguish between homozygous and heterozygous SNVs you
   will have to extend the format to include a format and a sample column
   with genotype (GT) information like in this example::

     #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sampleX
     chrI	1897409	.	A	G	.	.	.	GT	1/1
     chrI	1897492	.	C	T	.	.	.	GT	0/1
     chrI	1897616	.	C	A	.	.	.	GT	0/1
     chrI	1897987	.	A	T	.	.	.	GT	0/1
     chrI	1898185	.	C	T	.	.	.	GT	0/1
     chrI	1898715	.	G	A	.	.	.	GT	0/1
     chrI	1898729	.	T	C	.	.	.	GT	0/1
     chrI	1900288	.	T	A	.	.	.	GT	0/1
  
   , in which sampleX would be heterozygous for all SNVs except the first.

.. class:: warningmark
   
   If the optional VCF input contains INDEL calls, these will be ignored by the
   tool.

@HELP_FOOTER@
    ]]></help>
    <expand macro="citations" />
</tool>