annotate confab.xml @ 5:119b462f0f69 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit ed9b6859de648aa5f7cde483732f5df20aaff90e

<tool id="ctb_confab" name="Conformer calculation" version="0.4">
    <description>for molecules (confab)</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <requirements>
        <requirement type="package" version="2.4.1">openbabel</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[

    obabel
        '${infile}'
        -O '${outfile}'
        -i ${infile.ext}
        -o sdf
        --confab
        --verbose
        --rcutoff $RMSD
        --ecutoff $energy
        --conf $conformers
        $first_conformer

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates in SDF or MOL2 format" help="Dataset missing? See TIP below"/>
        <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (Å)' help='Minimum RMSD deviation from the original conformation in order to be classified as a separate conformer.'/>
        <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' help='Minimum energy difference to the original conformation in order to be classified as a separate conformer.'/>
        <param name='conformers' type='integer' value='1000000' label='Max number of conformers to test' />
        <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
            label='Include the input conformation as the first conformer' help='If yes, the original conformation is included in the output file'/>
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value='CID_3033.sdf' ftype='sdf' />
            <param name='RMSD'  value='0.5' />
            <param name='energy' value='50.0' />
            <param name='conformers' value='10' />
            <param name='first_conformer' value="True" />
            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/>
        </test>
    </tests>
<help>
<![CDATA[

.. class:: infomark

**What this tool does**

Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialization steps, is used to generate multiple conformers, which are filtered on-the-fly to identify diverse low-energy conformers.

.. _Confab: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html#confab

-----

.. class:: infomark

**Input**

* Example::

	21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
	21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
	22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
	21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
	23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
	23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
	24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0

	.......

	1  2  1  0  0  0  0
	1 11  1  0  0  0  0
	2  3  1  0  0  0  0
	3  4  2  0  0  0  0
	3  5  1  0  0  0  0
	5  6  2  0  0  0  0
	6  7  1  0  0  0  0

	RMSD cutoff (in Angstrom)	0.5
	Energy cutoff (in kcal/mol)	50.0
	Max number of conformers to test	100000
	Include the input conformation as the first conformer	False

-----

.. class:: infomark

**Output**

* Example::

     23 26  0  0  0  0  0  0  0  0999 V2000
   21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.4490    8.6370   60.4430 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7890    9.9970   60.0980 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.4340   10.0950   60.8720 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.6140   10.0230   62.4340 C   0  0  1  0  0  0  0  0  0  0  0  0
   21.6330   11.3540   60.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4320   11.4340   58.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7860   11.4040   58.1690 C   0  0  1  0  0  0  0  0  0  0  0  0
   23.4830   10.0600   58.5980 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.6740    9.9180   57.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0720   10.4500   56.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7140   11.1490   56.6270 C   0  0  2  0  0  0  0  0  0  0  0  0
   23.6590   12.6770   58.4540 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4270   11.2460   63.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3750   12.3880   55.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2120   12.8760   55.0520 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.0090   12.9760   55.8570 C   0  0  0  0  0  0  0  0  0  0  0  0

::

  1  2  1  0  0  0  0
  1 11  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  6  0  0  0
 10  9  1  1  0  0  0



]]>
    </help>
    <citations>
        <citation type="doi">10.1186/1758-2946-3-33</citation>
        <citation type="doi">10.1186/1758-2946-3-8</citation>
    </citations>
</tool>