view modify/change_title_to_metadata_value.xml @ 2:125da3a296ca draft default tip

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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="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command interpreter="python">
<![CDATA[
        ## 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>
<![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>
</tool>