annotate get_pubchem_as_smiles.xml @ 0:cd19c3fab3a6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb

<tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" version="0.2" >
    <description>as canonical SMILES</description>
    <requirements>
        <requirement type="package" version="2.4.1">openbabel</requirement>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <stdio>
        <regex match="obError"
               source="both"
               level="fatal"
               description="Critical Open Babel error" />
        <regex match="obWarning"
               source="both"
               level="warning"
               description="Non-critical Open Babel warning" />
        <regex match="obInfo"
               source="both"
               level="log"
               description="Open Babel Information" />
    </stdio>
    <command>
<![CDATA[
        python '$__tool_directory__/get_pubchem_as_smiles.py'
            -o $pubchem_smi
            -p \${GALAXY_SLOTS:-4}
            ## temporary hack until my Galaxy patch is committed
            > /dev/null 2>&1
]]>
    </command>
    <inputs>
    </inputs>
    <outputs>
        <data format="smi" name="pubchem_smi" />
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.

.. _PubChem: http://pubchem.ncbi.nlm.nih.gov/

-----

.. class:: infomark

**Output**

The output will be one large SMILES file.

]]>
    </help>
</tool>