view qiskit_xyz2pdb.xml @ 0:7372df4e8513 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 02ff1748664d6b2729209b6bf1ef17ff81f6b290

<tool id="qiskit_xyz2pdb" name="Convert Qiskit's XYZ files to" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>alpha carbon PDB files</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.2</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="0.1.2">qiskit-xyz2pdb</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
    #if $output_format == "hetatm":
    qiskit-xyz2pdb --in-xyz ./structure_input.${structure_input.ext} --hetero-atoms 
    #end if

    #if $output_format == "alpha_carbon_trace":
    qiskit-xyz2pdb --in-xyz ./structure_input.${structure_input.ext} --alpha-c-traces 
    #end if
    
    ]]></command>
    <inputs>
        <param name="structure_input" type="data" format="xyz" label="XYZ Structure file" help="In XYZ format. This file should be the initial output from the quantum algorithm, containing the coarse grain coordinates in XYZ format."/>
        <param name="output_format" type="select" label="Output format">
            <option value="alpha_carbon_trace">Alpha carbon trace file (generic alpha carbon trace format with no CONNECT lines)</option>
            <option value="hetatm">HETATM (generic heterogenous atom format with CONNECT lines representing bonds)</option>
        </param>
    </inputs>
    <outputs>
        <data name="output1" format="pdb" from_work_dir="*.pdb" label="Converted PDB file on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="structure_input" value="structure_input.xyz"/>
            <param name="output_format" value="hetatm" />
            <output name="output1" ftype="pdb">
                <assert_contents>
                    <has_text text="HETATM    1  R   PEP     1       0.000   0.000   0.000  1.00  0.00           R"/>
                    <has_text text="HETATM    2  H   PEP     2       2.194   2.194  -2.194  1.00  0.00           H"/>
                    <has_text text="HETATM    3  Y   PEP     3       4.388   0.000  -4.388  1.00  0.00           Y"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="structure_input" value="structure_input.xyz"/>
            <param name="output_format" value="alpha_carbon_trace" />
            <output name="output1" ftype="pdb">
                <assert_contents>
                    <has_text text="ATOM      1  CA  ARG     1       0.000   0.000   0.000  1.00  0.00           R"/>
                    <has_text text="ATOM      2  CA  HIS     2       2.194   2.194  -2.194  1.00  0.00           H"/>
                    <has_text text="ATOM      3  CA  TYR     3       4.388   0.000  -4.388  1.00  0.00           Y"/>
                </assert_contents>
            </output>
        </test>
    </tests>
        <help><![CDATA[

        .. class:: infomark
        
        **What it does**
        
        This tool takes the XYZ files from Qiskit's protein folding algorithm and converts them to a proper alpha carbon PDB file.
        
_____
        
        .. class:: infomark
        
        **Input**
        
               - XYZ file of coarse grain model coordinates
        
        
_____
        
        
        .. class:: infomark
        
        **Output**
        
               - Alpha carbon PDB file in either trace or HETATM format
        
            ]]></help>
        <citations>
            <citation type="bibtex">@misc{pypiQiskitxyz2pdb,
                author = {},
                title = {qiskit-xyz2pdb --- pypi.org},
                howpublished = {\url{https://pypi.org/project/qiskit-xyz2pdb/#history}},
                year = {},
                note = {[Accessed 22-05-2024]},
            }</citation>
        </citations>
</tool>