annotate bam_bed_gff_to_bigwig.xml @ 1:49c6f715bc82 draft

planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/

<tool id="bbgtobigwig" name="Convert BAM/BED/GFF to BigWig" version="0.1" profile="22.05"> 
    <requirements>
        <requirement type="package" version="455">ucsc-bedgraphtobigwig</requirement>
        <requirement type="package" version="2.31.1">bedtools</requirement>
        <requirement type="package" version="9.5">coreutils</requirement> 
        <requirement type="package" version="3.12.3">python</requirement>
    </requirements>
    <required_files>
        <include path="gff_to_bed_converter.py"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[
#if $hist_or_builtin.genosrc == "indexed":
    ln -s '$hist_or_builtin.chromfile.fields.len_path' ./CHROMFILE &&
#else:
    ln -s '$chromfile' ./CHROMFILE &&
#end if
#if $input1.ext in ['gff', 'gff3']:
    python '$__tool_directory__/gff_to_bed_converter.py' < '$input1' > input2 && 
#else:
    ln -s '$input1' input2 &&
#end if
#if $input1.ext == "bam":
    bedtools genomecov -bg -split -ibam input2 | 
#else
    bedtools genomecov -bg -i input2 -g ./CHROMFILE |
#end if
LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg &&
bedGraphToBigWig temp.bg ./CHROMFILE '$output'
    ]]></command>
    <inputs>
        <conditional name="hist_or_builtin">
            <param name="genosrc" type="select" label="Is the input assigned to a built-in or custom reference genome?" 
                help="If the input has no dbkey, supply a chromosome lengths file">
                <option selected="True" value="indexed">Input data was made with a built-in genome or already has a custom genome dbkey</option>
                <option value="history">Input data mapped on a genome from the current history. The chromosome lengths file is also in the history</option>
            </param>
            <when value="indexed">
                <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert">
                    <validator type="unspecified_build" />
                </param>
                <param name="chromfile" type="select" label="Source Genome Build">
                    <options from_data_table="__dbkeys__">
                        <filter type="data_meta" column="0" key="dbkey" ref="input1"/>
                    </options>
                    <validator type="no_options" message="The chosen genome build is not available."/>
                </param>
            </when>
            <when value="history">
                <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert"/>
                <param name="chromfile" type="data" format="len,txt,tabular" label="Chromosome length file" 
                   help="Sequence lengths for the history reference are required to make a bigwig. Compute sequence length tool makes these from fasta files"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="bigwig"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="hist_or_builtin">
                <param name="genosrc" value="indexed"/>
                <param name="input1" value="featureCounts_input1.bam" dbkey="hg38"/>
                <param name="chromfile" value="hg38"/>
            </conditional>
            <output name="output" value="featureCounts_input1.bigwig" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <conditional name="hist_or_builtin">
                <param name="genosrc" value="history"/>
                <param name="input1" value="srma_out2.bam"/>
                <param name="chromfile" value="testing.len"/>
            </conditional>
            <output name="output" value="srma_out2.bigwig" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <conditional name="hist_or_builtin">
                <param name="genosrc" value="history"/>
                <param name="input1" value="test5.gff3"/>
                <param name="chromfile" value="testing.len"/>
            </conditional>
            <output name="output" value="test5.gff.bigwig" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <conditional name="hist_or_builtin">
                <param name="genosrc" value="history"/>
                <param name="input1" value="test5.bed"/>
                <param name="chromfile" value="testing.len"/>
            </conditional>
            <output name="output" value="test5.bed.bigwig" compare="sim_size"/>
        </test>
    </tests>
    <help>

   Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
 
   If the input does not have a dbkey, a chromosome lengths file must be provided. The actual reference is not needed.
 
   This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey.

    </help>    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq351</citation>
    </citations>
</tool>