annotate bcftools_view.xml @ 2:14567aa2be12 draft default tip

Added wrapper script for correct stderr handling

<tool id="bcftools_view" name="bcftools view" version="1.0.0">
    <description>Converts BCF format to VCF format</description>
    <requirements>
        <requirement type="package" version="0.1.18">samtools</requirement>
    </requirements>
    <command interpreter='python'>
        bcftools_wrapper.py bcftools view 
            #if str( $A ) == "true": 
                -A
            #end if
            #if str( $b ) == "true":
                -b
            #end if
	    #if $D.seq_dictionary == "true":
                -D "$D.input"
	    #end if
            #if str( $F ) == "true":
                -F
	    #end if
            #if str( $G ) == "true":
                -G
	    #end if
            #if str( $N ) == "true":
                -N
	    #end if
            #if str( $S ) == "true":
                -S
	    #end if
            #if str( $u)  == "true":
                -u
	    #end if
            #if str( $c ) == "true":
                -c
	    #end if
            #if str( $e ) == "true":
                -e
	    #end if
            #if str( $g ) == "true":
                -g
	    #end if
            #if $i.alt_indel_snp_ratio == "true":
                -i $i.ratio
	    #end if
            #if $p.variant_filter == "true":
                -p $p.float_value
	    #end if
            #if $t.mutation_rate == "true":
                -t $t.rate
	    #end if
            #if str( $v ) == "true":
                -v
	    #end if	
	$input
        > $output 
    </command>
    <inputs>
        <param name="input" type="data" format="bcf" label="Choose a bcf file to view" />
        <param name="A" type="select" label="Retain all possible alternate alleles at variant sites">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="b" type="select" label="Output in the BCF format. The default is VCF.">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <conditional name="D">
            <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion.">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param name="input" type="data" format="tabular" label="Sequence dictionary" />
            </when>
        </conditional>
        <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different).">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="G" type="select" label="Suppress all individual genotype information.">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="S" type="select" label="The input is VCF instead of BCF.">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="u" type="select" label="Uncompressed BCF output.">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only">
            <option value="true" selected="true">Yes</option>
            <option value="false">No</option>
        </param>
        <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT.">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <param name="g" type="select" label="Call per-sample genotypes at variant sites">
            <option value="true" selected="true">Yes</option>
            <option value="false">No</option>
        </param>
        <conditional name="i">
            <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15.">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param name="ratio" type="float" label="Ratio (float)" value="0.15" />
            </when>
        </conditional>
        <conditional name="p">
            <param name="variant_filter" type="select" >
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param name="float_value" type="float" label="Float" value="0.5" />
            </when>
        </conditional>
	<conditional name="t">
            <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001.">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>
            </param>
            <when value="true">
                <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" />
            </when>
        </conditional>
        <param name="v" type="select" label="Output variant sites only.">
            <option value="true" selected="true">Yes</option>
            <option value="false">No</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <help>
**What it does:** 

This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities:

http://samtools.sourceforge.net/samtools.shtml#4

------

**Citation:**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_


If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert.  CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__

    .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html

Correspondence to [e-mail] (G.M.) or [e-mail] (O.H.)

    </help>
</tool>