view BioPDB_align_and_rmsd.xml @ 0:6352d6dd74e2 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668

<tool id="biopdb_align_and_rmsd" name="Align structures and compute relative RMSDs" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using Biopython</description>
    <macros>
        <token name="@TOOL_VERSION@">1.79</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="1.79">biopython</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    python3 '$__tool_directory__/BioPDB_align_and_rmsd.py' --start_residue '$start_residue' --end_residue '$end_residue' --ref_structure '$ref_structure' --model '$model' --aligned_structure '$aligned_structure' --rmsd '$rmsd_out' >> verbose.txt 2>&1
    
    ]]></command>
    <inputs>
        <param name="start_residue" type="integer" label="Starting residue to align" help="This should be the same starting residue for the model and reference structure." value="0" />
        <param name="end_residue" type="integer" label="Ending residue to align" help="This should be the same ending residue for the model and reference structure." value="0"/>
        <param name="ref_structure" type="data" format="pdb" label="Reference structure" help="This can be an experimental structure or another model you wish to compare against."/>
        <param name="model" type="data" format="pdb" label="Sample structure" help="This is the structure you wish to align and compute a relative RMSD for. This can also be an experimental structure or another model."/>
    </inputs>

    <outputs>
        <data name="aligned_structure" format="pdb" label="PDB file of the aligned structure ${on_string}"></data>
        <data name="rmsd_out" format="tabular" label="RMSD of the aligned structure ${on_string}"></data>
    </outputs>

    <tests>
        <test>
            <param name="start_residue" value="1" />
            <param name="end_residue" value="15"/>
            <param name="ref_structure" value="reference_structure.pdb" />
            <param name="model" value="model.pdb" />
            <output name="aligned_structure" ftype="pdb">
                <assert_contents>
                    <has_text text="ATOM      5  CA  ARG     1       6.016   6.125  -0.066  1.00  0.00           C"/>
                    <has_text text="ATOM     29  CA  HIS     2       4.909   5.168   3.434  1.00  0.00           C"/>
                    <has_text text="ATOM     46  CA  TYR     3       7.956   4.326   5.551  1.00  0.00           C"/>
                </assert_contents>
            </output>
            <output name="rmsd_out" ftype="tabular">
                <assert_contents>
                    <has_text text="5.492787964992471"/>
                </assert_contents>
            </output>
        </test>
    </tests>

        <help><![CDATA[
Tool to align protein structures and compute relative RMSDs, using the alpha carbon coordinates.

.. class:: infomark

**Inputs**

PDB files for the reference structure, a model, as well as the starting and ending residues for the alignment.

.. class:: infomark

**Outputs**

1) Tabular file containing the RMSD.
2) PDB file of the model with the aligned coordinates.


        ]]></help>
    <citations>
        <citation type="doi">https://doi.org/10.1093/bioinformatics/btp163</citation>
    </citations>
</tool>