annotate docking.xml @ 2:18dec59e29ae draft

planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9

<tool id="docking" name="Docking" version="0.1.0">
    <description>- Tool to running molecular docking with Autodock Vina</description>
    <requirements>
        <requirement type="package" version="1.1.2">autodock-vina</requirement>
    </requirements>
    <stdio>
        <exit_code range="1" />
    </stdio>
    <command><![CDATA[
        vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2"
    ]]></command>
    <inputs>
        <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" />
        <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" />
        <param type="data" name="ligand" format="pdbqt"  label="Ligand: " help="Select a ligand pdbqt file" />
    </inputs>
    <outputs>
        <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" />
        <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.log" />
    </outputs>
    <tests>
        <test>
            <param name="box" value="config_complexo_dm.txt"/>
            <param name="receptor" value="3u1i_for_DM.pdbqt"/>
            <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
            <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
            <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
        </test>
    </tests>
    <help><![CDATA[
        ** What it does? **

        This tool performs molecular docking with Autodock Vina program.

        ** inputs **

        Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example:

        size_x =  20.00
        size_y =  18.40
        size_z =  23.60
        center_x =  70.92
        center_y =  70.57
        center_z =  36.86
        num_modes = 9999
        energy_range = 9999
        exhaustiveness = 10
        cpu = 4
        seed = 1

        Where the parameters size_x, size_y, size_z, center_x, center_y and center_z  are coordinates of the binding site. 
        The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.

        The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
        The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.

        ** outputs **

        Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example:

        MODEL 1
        REMARK VINA RESULT:      -0.0      0.000      0.000
        REMARK  9 active torsions:
        REMARK  status: ('A' for Active; 'I' for Inactive)
        REMARK    1  A    between atoms: C_2  and  O_3 
        REMARK    2  A    between atoms: C_2  and  C_14 
        REMARK    3  A    between atoms: O_3  and  C_4 
        REMARK    4  A    between atoms: C_4  and  C_5 
        REMARK    5  A    between atoms: C_6  and  C_8 
        REMARK    6  A    between atoms: C_8  and  C_9 
        REMARK    7  A    between atoms: C_9  and  C_10 
        REMARK    8  A    between atoms: C_16  and  O_17 
        REMARK    9  A    between atoms: C_19  and  O_20 
        ROOT
        ATOM      1  O   LIG d   1      72.801  71.157  37.352  0.00  0.00    -0.259 OA
        ATOM      2  C   LIG d   1      73.413  72.112  37.794  0.00  0.00     0.293 C 
        ENDROOT
        BRANCH   2   3
        ATOM      3  O   LIG d   1      72.912  73.321  38.144  0.00  0.00    -0.314 OA
        BRANCH   3   4
        ATOM      4  C   LIG d   1      71.868  73.332  39.120  0.00  0.00     0.206 C 
        BRANCH   4   5
        ATOM      5  C   LIG d   1      72.522  73.555  40.453  0.00  0.00     0.002 C 
        ATOM      6  C   LIG d   1      72.762  72.629  41.405  0.00  0.00    -0.085 C 
        ATOM      7  C   LIG d   1      72.390  71.176  41.274  0.00  0.00     0.043 C 
        BRANCH   6   8
        ATOM      8  C   LIG d   1      73.435  73.012  42.714  0.00  0.00     0.037 C 
        BRANCH   8   9
        ATOM      9  C   LIG d   1      74.184  74.348  42.631  0.00  0.00     0.031 C 
        BRANCH   9  10
        ATOM     10  C   LIG d   1      75.668  74.175  42.431  0.00  0.00    -0.024 C 
        ATOM     11  C   LIG d   1      76.399  74.547  41.360  0.00  0.00    -0.091 C 
        ATOM     12  C   LIG d   1      75.833  75.151  40.104  0.00  0.00     0.042 C 
        ATOM     13  C   LIG d   1      77.897  74.373  41.339  0.00  0.00     0.042 C 
        ENDBRANCH   9  10
        ENDBRANCH   8   9
        ENDBRANCH   6   8
        ENDBRANCH   4   5
        ENDBRANCH   3   4
        ENDBRANCH   2   3
        BRANCH   2  14
        ATOM     14  C   LIG d   1      74.882  72.132  38.012  0.00  0.00     0.042 A 
        ATOM     15  C   LIG d   1      75.732  72.845  37.153  0.00  0.00     0.057 A 
        ATOM     16  C   LIG d   1      77.101  72.826  37.385  0.00  0.00     0.099 A 
        ATOM     17  C   LIG d   1      77.623  72.116  38.462  0.00  0.00     0.098 A 
        ATOM     18  C   LIG d   1      76.791  71.422  39.330  0.00  0.00     0.040 A 
        ATOM     19  C   LIG d   1      75.412  71.432  39.110  0.00  0.00     0.020 A 
        BRANCH  16  20
        ATOM     20  O   LIG d   1      77.978  73.498  36.578  0.00  0.00    -0.358 OA
        ATOM     21  HO  LIG d   1      77.680  74.093  35.900  1.00  0.00     0.217 HD
        ENDBRANCH  16  20
        BRANCH  17  22
        ATOM     22  O   LIG d   1      78.971  72.100  38.675  0.00  0.00    -0.358 OA
        ATOM     23  HO  LIG d   1      79.541  71.651  38.060  1.00  0.00     0.217 HD
        ENDBRANCH  17  22
        ENDBRANCH   2  14
        TORSDOF 9
        ENDMDL 

        The last is a log file with the binding affinity scores, this file looks like the following example:

        -----------------------------------------------------------------
         If you used AutoDock Vina in your work, please cite:          
                                                                       
         O. Trott, A. J. Olson,                                        
         AutoDock Vina: improving the speed and accuracy of docking    
         with a new scoring function, efficient optimization and       
         multithreading, Journal of Computational Chemistry 31 (2010)  
         455-461                                                       
                                                                       
         DOI 10.1002/jcc.21334                                         
                                                                       
         Please see http://vina.scripps.edu for more information.      
        ------------------------------------------------------------------

        Reading input ... done.
        Setting up the scoring function ... done.
        Analyzing the binding site ... done.
        Using random seed: 1899908181
        Performing search ... done.
        Refining results ... done.

        mode |   affinity | dist from best mode
             | (kcal/mol) | rmsd l.b.| rmsd u.b.
        -----+------------+----------+----------
           1         -0.0      0.000      0.000
           2         -0.0      2.046      2.443
           3         -0.0      5.896      7.949
           4         -0.0      2.518      3.100
           5         -0.0      2.417      4.527
           6         -0.0      5.686      7.689
           7         -0.0      2.828      4.792
           8         -0.0      5.547      7.086
           9         -0.0      7.388      9.966
          10         -0.0      7.877     11.352
          11         -0.0      8.203     10.157
          12         -0.0      5.163      7.653
          13         -0.0      3.093      6.011
          14         -0.0      7.998     11.146
          15         -0.0      7.015     10.108
          16         -0.0      8.795     11.682
          17         -0.0      7.317     10.367
          18          0.0      3.274      4.160
          19          0.0     10.286     12.001
          20          0.0      3.566      5.349
        Writing output ... done.
    ]]></help>
    <citations>
        <citation type="doi">10.1002/jcc.21334</citation>
    </citations>
</tool>