view fasta-stats.xml @ 2:cd0874854f51 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"

<tool id="fasta-stats" name="Fasta Statistics" version="1.0.2">
    <description>Display summary statistics for a fasta file.</description>
    <requirements>
        <requirement type="package" version="5.26">perl</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        perl '${__tool_directory__}/fasta-stats.pl'
        '$dataset'
        #if $genome_size:
            $genome_size
        #end if
        > '$stats'
        ]]>
    </command>
    <inputs>
        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
        <param name="genome_size" type="float" optional="True" label="Genome size estimate (optional)" help="Estimate of the genome size in bases. If specified, NG50 and LG50 will be calculated."/>
    </inputs>
    <outputs>
        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
    </outputs>
    <tests>
        <test>
            <param name="dataset" value="test.fasta"/>
            <output name="stats" file="test_out.txt"/>
        </test>
        <test>
            <param name="dataset" value="ng50_input.fasta"/>
            <param name="genome_size" value="4000"/>
            <output name="stats" file="ng50_out.txt"/>
        </test>
    </tests>
    <help>
**Fasta Stats**
Displays the summary statistics for a fasta file.

------

Outputs in tabular form:
    Lengths: n50, min, max, median and average

    Number of base pairs: A, C, G, T, N, Total and Total_not_N

    Number of sequences

    GC content in %

    If an optional genome size estimate is specified, then the NG50 length will also be calculated. 

------

Inputs:

Fasta dataset
    </help>
    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Seemann_Gladman2012,
    author = {Torsten Seemann and Simon Gladman},
    title = {Fasta Statistics: Display summary statistics for a fasta file.},
    year = {2012},
    url = {https://github.com/galaxyproject/tools-iuc},
}
        </citation>
    </citations>
</tool>