view glimmer_acgt_content.xml @ 0:4c74f770979d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a

<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@">
    <description>of windows in each sequence</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        window-acgt
            $percentage
            $input_win_len
            $input_win_skip
            < '$infile' > '$output'

            ##TODO prettify the output
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Genome Sequence"/>
        <param name="input_win_len" type="integer" value="10" label="The width of the sliding window"/>
        <param name="input_win_skip" type="integer" value="10" label="The number of positions between windows to report"/>
        <param name="percentage" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Report percentages instead of counts"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="streptomyces_Tu6071_genomic.fasta" />
            <output name="output" file="streptomyces_Tu6071_genomic.acgt" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

This tool calculates the ACGT-Content from a given Sequence, given a sliding window.

-------

**Output**

Output is in the format:

	window-start	window-len	A's	C's	G's	T's	#other	%GC

Note the last window in the sequence can be shorter than *window-len* if the sequence ends prematurely
]]>
    </help>
    <expand macro="citation" />
</tool>