view protein_properties.xml @ 0:cd211b8c2e51 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties commit 6767a5ffb02052c844e9d862c79912f998f39d8e

<tool id="bg_protein_properties" name="Calculate protein properties" version="0.1.0">
    <description></description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        '$__tool_directory__/protein_properties.py' < '$input' > '$output'
    ]]></command>
    <inputs>
        <param format="fasta" name="input" type="data" label="Protein sequence"
            help="This should be in FASTA format." />
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="Q9LHB9.fasta" ftype="fasta"/>
            <output name="output" file="protein_properties_result1.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**
 
This tool will calculate several properties for each given input sequence. The result will contain the following columns:

- ID of the sequence
- Molecular weight
- Isoelectric point
- *gravy* according to Kyte and Doolittle
- Length of the sequence
- Instability index, according to Guruprasad, 1990. (Any value above 40 means the protein is unstable (has a short half life))
- Aromaticity, according to Lobry, 1994. (It is simply the relative frequency of Phe+Trp+Tyr)
- Sequence (as given in the input)

For more information see the `BioPython ProteinAnalysis documentation <http://www.biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html>`_.

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp163</citation>
    </citations>
</tool>