view pulchra.xml @ 0:212ccef97a3a draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5

<tool id="pulchra" name="PULCHRA recontruction of all atom proteins" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="22.05">
    <description>from reduced representations</description>
    <macros>
        <token name="@TOOL_VERSION@">3.06</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pulchra</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
	pulchra 
	
	##inputs
	./structure_input.${structure_input.ext}
     $skip_sidechain

    -v
 
    ]]></command>
    <inputs>
        <param name="structure_input" type="data" format="pdb" label="Structure file" help="In PDB format. This input is usually an 'alpha trace' or other incomplete structure file."/>
        <param argument="-s" name="skip_sidechain" type="boolean" truevalue="-s" falsevalue="" label="Skip sidechain reconstruction?" help="By default, both sidechains and backbone will be reconstructed otherwise."/>
    </inputs>
    <outputs>
        <data name="output1" format="pdb" from_work_dir="*.rebuilt.pdb" label="PULCHRA rebuilt pdb file on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="structure_input" value="model.pdb"/>
            <output name="output1" ftype="pdb">
                <assert_contents>
                    <has_text text="ATOM      1  N   PHE     1      16.391  50.300  23.791"/>
                    <has_text text="ATOM     12  N   LEU     2      14.039  47.806  25.433"/>
                    <has_text text="ATOM     20  N   VAL     3      10.836  47.425  24.846"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="structure_input" value="model.pdb"/>
            <param name="skip_sidechain" value="true" />
            <output name="output1" ftype="pdb">
                <assert_contents>
                    <has_text text="ATOM      1  N   PHE     1      16.391  50.300  23.791"/>
                    <has_text text="ATOM     12  O   VAL     3       8.414  45.957  24.602"/>
                    <has_text text="ATOM     20  O   MET     5       1.327  47.936  26.198"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

        .. class:: infomark
        
        **What it does**
        
        This tool rebuilds a protein structure from reduced representations (alpha carbon trace), producing an all-heavy atom PDB file.
        
_____
        
        .. class:: infomark
        
        **Input**
        
               - Alpha carbon trace PDB file
        
        
_____
        
        
        .. class:: infomark
        
        **Output**
        
               - Rebuilt all-heavy atom PDB file
        
            ]]></help>
        <citations>
            <citation type="doi">10.1002/jcc.20906</citation>
        </citations>
</tool>