view fasplit.xml @ 3:d3f58a0dc09d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162

<tool id="fasplit" name="faSplit" version="@TOOL_VERSION@" profile="22.05">
    <description>Split a FASTA file</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-fasplit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
mkdir out &&
faSplit
$O.split_type
'$input'
#if $O.split_type != 'byname'
    $O.count
#end if
out/
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="FASTA file" />
        <conditional name="O">
            <param name="split_type" type="select" label="Split by:">
                <option value="sequence" selected="true">Number of files (for multi sequence FASTA)</option>
                <option value="base">Number of files (for single sequence FASTA)</option>
                <option value="size">Number of base (for single sequence FASTA)</option>
                <option value="byname">By name</option>
            </param>
            <when value="sequence">
                <param name="count" type="integer" value="10" label="Number of chunks" />
            </when>
            <when value="base">
                <param name="count" type="integer" value="10" label="Number of chunks" />
            </when>
            <when value="size">
                <param name="count" type="integer" value="100" label="Size of chunks (bp)" />
            </when>
            <when value="byname" />
        </conditional>
    </inputs>
    <outputs>
        <collection name="output_list" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" ext="fasta" directory="out"/>
        </collection>
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="fasta" value="CDS.fa" />
            <param name="split_type" value="sequence" />
            <param name="count" value="5" />
            <output_collection name="output_list" type="list">
                <element name="0" file="0.fa" />
                <element name="1" file="1.fa" />
                <element name="2" file="2.fa" />
                <element name="3" file="3.fa" />
                <element name="4" file="4.fa" />
            </output_collection>
        </test>
        <test>
            <param name="input" ftype="fasta" value="CDS.fa"/>
            <param name="split_type" value="byname"/>
            <output_collection name="output_list" type="list">
                <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" />
                <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
                <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
                <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
                <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
                <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
                <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
                <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
                <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
                <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
                <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
                <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
                <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
                <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" />
                <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
                <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
                <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
                <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
                <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
                <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
                <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
                <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
                <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
                <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
                <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
                <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
                <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
                <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
                <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
                <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" />
                <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" />
                <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" />
                <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" />
                <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" />
                <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" />
                <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" />
                <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" />
                <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" />
                <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`faSplit`_ is a tool to split a single FASTA file into several files.

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

.. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/faSplit/faSplit.c
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>