annotate ob_remSmall.xml @ 13:e94b2920d4e4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"

<tool id="openbabel_remSmall" name="Remove small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from a library of compounds</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    obabel
      -i"${infile.ext}"
      '${infile}'
      -ocopy
      -O '${outfile}'
      --filter "atoms > $cutoff"
      -e
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <param name="cutoff" type="integer" value="5"
            label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="3_mol.smi" />
            <param name="cutoff" value="5" />
            <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Filters a library of compounds and removes small molecules below a predefined input number of atoms.

-----

.. class:: warningmark

**Hint**

Some libraries may contain molecules without a 1D/3D descriptor, which may provoke crashes of any other tool. It is strongly advised to run this tool before proceeding to any further steps.

-----

.. class:: infomark

**Output**

Same as input format.



]]>
    </help>
    <expand macro="citations"/>
</tool>