view change_title_to_metadata_value.xml @ 3:e91b7324bb40 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c376ab981fafb25f0c04a2a313968fa2e55f5196

<tool id="openbabel_change_title" name="Change Title" version="@VERSION@.0">
    <description>to meta-data value.</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>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
        python '$__tool_directory__/change_title_to_metadata_value.py'
            --infile '${infile}'
            --key '${key}'
            --outfile '${outfile}'
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/>
        <param name="key" type="text" format="text" label="Compound Identifier encoded in the SDF file." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/>
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="sdf" value="CID_3033.sdf"/>
            <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
            <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Changes the title of a molecule file to a metadata value of a given ID in the same molecule file.

-----

.. class:: infomark

**Input**

`SD-file`_ with metadata including the given ID.

.. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file

-----

.. class:: infomark

**Output**

Same as input with changed title tag.


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