view change_title_to_metadata_value.xml @ 1:6e3671604a4a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 63d8775d73dd16e3ee8836ea8c06c81801e87c71

<tool id="ctb_change_title" name="Change Title" version="0.0.1">
    <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="output" 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.

-----

.. class:: infomark

**Cite**

`Open Babel`_

.. _Open Babel: http://openbabel.org/wiki/Main_Page

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