view shuffling.xml @ 2:f29e21388219 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2

<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.1">
    <description></description>
    <macros>
        <import>vsearch_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    vsearch
        @GENERAL@
        --output "$outfile"
        --seed "$seed"
        --shuffle "$infile"
        #if str( $topn ):
            --topn "$topn"
        #end if
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" />
        <param name="seed" type="integer" value="0" label="Seed"
            help="Zero to use random data source. (--seed)"/>
        <expand macro="topn" />
    </inputs>
    <outputs>
        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta" />
            <param name="seed" value="1"/>
            <param name="topn" value="5"/>
            <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Sequence shuffling to obtain new random sequences.

Shuffling options
  --output FILENAME           output to specified FASTA file
  --seed INT                  seed for PRNG, zero to use random data source (0)
  --shuffle FILENAME          shuffle order of sequences pseudo-randomly
  --topn INT                  output just first n sequences


@EXTERNAL_DOCUMENTATION@


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