view ob_remSmall.xml @ 13:e94b2920d4e4 draft

"planemo upload for repository commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:44:19 +0000
parents aebc671bae78
line wrap: on
line source

<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-->
        <token name="@GALAXY_VERSION@">0</token>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
      -O '${outfile}'
      --filter "atoms > $cutoff"
        <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)" />
        <expand macro="output_like_input"/>
            <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" />

.. class:: infomark

**What this tool does**

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


.. class:: warningmark


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


Same as input format.

    <expand macro="citations"/>