annotate end-to-end.xml @ 1:ce9dc91ff87f draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"

<tool id="mdanalysis_endtoend" name="End-to-End Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- End-to-End distance timeseries and histogram for the given selections</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/end-to-end.py'
        --itraj '$trajin'
        --istr '$strin'
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1 '$segid1'
        --ilabel '$label1'
        --ititle1 '$title1'
        --output1 '$output1'
        --o_plot '$o_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <param name="segid1" type="text" value="PROA" label="Segment ID of the protein" help="A valid segment ID selection for the current molecular system">
            <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
        </param>
        <param name="label1" type="text" value="N-C" label="Data series label">
            <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9\- ]{1,8}$</validator>
        </param>
        <param name="title1" type="text" value="End-to-End timeseries and histogram" label="Plot title" help="Plot title, to be included in image output">
            <validator type="regex" message="Maximum of 36 characters allowed.">^[a-zA-Z0-9\- ]{1,36}$</validator>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output1" label="timeseries raw data"/>
        <data format="png" name="o_plot" label="End-to-End Timeseries and Histogram Plot"/>
    </outputs>
    <tests>
        <test>
            <param name="trajin" value="test.dcd" ftype="dcd"/>
            <param name="strin" value="test.pdb" ftype="pdb"/>
            <param name="segid1" value="PRO"/>
            <output name="output1">
                <assert_contents>
                    <has_text text="3.921"/>
                    <has_text text="3.938"/>
                </assert_contents>
            </output>
            <output name="o_plot">
                <assert_contents>
                    <has_size value="39991" delta="3000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
.. class:: infomark

**What it does**

End-to-End distance timeseries and histogram for proteins. The termini are chosen as ends with the N atom of the N-terminus and the C atom of the C-terminus chosen.

_____


.. class:: infomark

**Input**

       - Trajectory file (DCD).
       - PDB file.
       - Segment ID for the protein
       - Graph series label and title

Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

_____


.. class:: infomark

**Output**

       - Tab-separated file of timeseries raw data
       - Image (as png) of the end-to-end timeseries and histogram

    ]]>
    </help>
    <expand macro="citations"/>
</tool>