view glimmer_acgt_content.xml @ 3:ce7228503d49

changes

<tool id="glimmer_acgt-content" name="ACGT Content" version="0.1">
    <description>of windows in each sequence</description>
    <requirements>
        <requirement type="package" version="3.02b">glimmer</requirement>
    </requirements>
    <command>
        window-acgt
            $percentage
            $input_win_len
            $input_win_skip
            &lt; $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_coelicolor.dna" />
            <output name="output" file="fasta_tool_convert_from_dna.out" />
        </test>
    </tests>
    <help>

**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




**References**

A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).


    </help>
</tool>