view modify/change_title_to_metadata_value.xml @ 8:fa78faf6ee4f

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<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>
    <requirements>
        <requirement type="python-module">pybel</requirement>
    </requirements>
    <command interpreter="python">
        ## The command is a Cheetah template which allows some Python based syntax.
        ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
        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>
        <data name="outfile" format_source="infile"/>
    </outputs>
    <tests>
        <param name="infile" type="sdf" value="CID_3033.sdf"/>
        <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
        <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/>
    </tests>
    <help>

.. class:: infomark

**Hint**

  To convert the output, use the pencil icon next to the history entry.

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**What it does**

Change the title from a molecule file to metadata value of a given-id of the same molecule file.

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**Input format**

SDF with metadata including the given key.

**Output format**

Same as input with changed title tag.

**References**


    </help>
</tool>