view maskFastaBed.xml @ 9:2ab422b551df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit bad476ff5076338f3eebdf0c25bb5a6c745e5592

<tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0">
    <description>use intervals to mask sequences from a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools maskfasta
            $soft
            -mc "${mc}"
            -fi "${fasta}"
            -bed "${input}"
            -fo "${output}"
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
        <param format="fasta" name="fasta" type="data" label="Fasta file"/>
        <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue=""
            label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
            help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" />
        <param name="mc" type="text"  value="N" length="1"
            label="Replace masking character"
            help="That is, instead of masking with Ns, use another character. (-mc)" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="soft" value="False" />
            <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="soft" value="True" />
            <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.

.. image:: $PATH_TO_IMAGES/maskfasta-glyph.png

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