view chainnet.xml @ 0:3a213e01bc7f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a

<tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
    <description>
        make alignment nets out of alignment chains
    </description>
    <macros>
        <token name="@TOOL_VERSION@">469</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainnet</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    chainNet
        '$in_chain'
        #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
            '${target_reference_index_source.in_tar_ref_index}'
        #else:
            '$target_reference_index_source.tar_ref_index_file.fields.path'
        #end if
        #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
            '${query_reference_index_source.in_que_ref_index}'
        #else:
            '$query_reference_index_source.que_ref_index_file.fields.path'
        #end if
        '$targetNet'
        '$queryNet'
        #if str($minSpace)
            -minSpace=$minSpace
        #end if
        #if str($minFill)
            -minFill=$minFill
        #end if
        #if str($minScore)
            -minScore=$minScore
        #end if
        $inclHap
        #if str($verbose)
            -verbose=$verbose
        #end if
    ]]></command>
    <inputs>
        <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" />

        <conditional name="target_reference_index_source">
            <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
                <option value="cached">Built-in</option>
                <option value="history">From history</option>
            </param>
            <when value="cached">
                <param name="tar_ref_index_file" type="select" label="Using reference genome index">
                  <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
            </when>
        </conditional>

        <conditional name="query_reference_index_source">
            <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index">
                <option value="cached">Built-in</option>
                <option value="history">From history</option>
            </param>
            <when value="cached">
                <param name="que_ref_index_file" type="select" label="Using reference genome index">
                  <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
            </when>
        </conditional>

        <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" />
        <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" />
        <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" />
        <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." />
        <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" />

    </inputs>
    <outputs>
        <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/>
        <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="in_chain" value="input.chain" />
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="history" />
                <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="history" />
                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
            </conditional>
            <output name="targetNet" file="target.net"/>
            <output name="queryNet" file="query.net"/>
        </test>
        <test expect_num_outputs="2">
            <param name="in_chain" value="input.chain" />
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="cached" />
                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="cached" />
                <param name="que_ref_index_file" value="mm39.chr2.chunk"/>
            </conditional>
            <output name="targetNet" file="target.net"/>
            <output name="queryNet" file="query.net"/>
        </test>
        <test expect_num_outputs="2">
            <param name="in_chain" value="input.chain" />
            <param name="minScore" value="1200" />
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="cached" />
                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="history" />
                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
            </conditional>
            <output name="targetNet" file="target.1200.net"/>
            <output name="queryNet" file="query.1200.net"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`chainNet`_ is a tool that makes alignment nets out of `alignment chains`_.
It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence.

For implementation details see ChainNet's `source code`_.

.. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
.. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>