view samtools_faidx/samtools_faidx.xml @ 0:e1fe804af4bd draft default tip

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<tool id="samtools_chrom_sizes" name="Samtools Chromosome Sizes" version="2.0.4" profile="@PROFILE@">
    <description>order of storing aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        samtools faidx '${input1}' --fai-idx '${output1}'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta" label="FASTA File" />
    </inputs>
    <outputs>
       <data name="output1" format="fai"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test.fasta" ftype="fasta" />
            <output name="output1" file="test.fasta.fai" ftype="fai" lines_diff="4" />
        </test>
    </tests>
    <help>
**What it does**

Creates a FAI index for a given FASTA file 
    </help>
    <expand macro="citations"/>
</tool>