view calculate_diameter.xml @ 1:658c6ec58e91 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"

<tool id="calculate_diameter" name="calculate pore diameter of AQP" version="0.1.0" python_template_version="3.5" profile="@GALAXY_VERSION@" >
    <macros>
        <token name="@GALAXY_VERSION@">21.05</token>
    </macros>
    <requirements>
        <requirement type="package" version="2.1.0">mdanalysis</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/calculate_pore_diameter_aqp.py'
            --arr_one '$arr1'
            --arr_second '$arr2'
            --gro_file '$gro_file'
            --xtc_file '$xtc_file'
            --gro_file_ext '$gro_file.ext'
            --xtc_file_ext '$xtc_file.ext'
            --output '$table'
            --verbose
            --log_output '$tool_log'
            --output_directory 'out'
            2>&1
    ]]></command>
    <inputs>
        <param name="gro_file" type="data" format="gro" optional="False" help="Put your .gro file"/>
        <param name="xtc_file" type="data" format="xtc" optional="False" help="Put your .xtc file"/>
        <param name="arr1" type="text"  optional="False" label="pattern1" help="Pattern1 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : HSD LEU ALA THR">
          <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator>
        </param>
        <param name="arr2" type="text" optional="False" label="pattern2" help="Pattern2 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : ARG SER PHE GLY">
          <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="table" format="tabular" from_work_dir="out/" label="${tool.name} (Tabular)"/>
        <data name="tool_log" format="txt" from_work_dir="out/*.log" label="${tool.name} (LOG)"/>
    </outputs>
    <tests>
        <test>
            <param name="gro_file" value="PIP2.1_test.gro" ftype="gro" />
            <param name="xtc_file" value="PIP2.1_test.xtc" ftype="xtc" />
            <param name="arr1" value="HSD LEU ALA THR"/>
            <param name="arr2" value="ARG SER PHE GLY"/>
            <output name="table" file="pair_dist_arr.tabular" />
            <output name="tool_log" file="calculate_pore_diameter_aqp.log" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool allows to launch a calculation of the pore diameter of an aquaporin as a function of time from a .gro file and an .xtc file. The calculation is made between the alpha carbons of two amino acids.

_____

.. class:: infomark

**Inputs**

       - gro_file : .gro file created with GROMACS containing the system coordinates.
       - xtc_file : .xtc file created during a GROMACS simulation containing the trajectory for a given time of the system.
       - pattern1 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code.
       - pattern2 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code.

_____

.. class:: infomark

**Outputs**

       - TSV file : contains all the distance measurements on a part of the trajectory and the average of these distances.
       - LOG file of the tool execution

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btz107</citation>
    </citations>
</tool>