<tool id="glytools_get_CFG_array" name="GAP Get CFG array" version="0.1.1">

    <description> download glycan metadata (and xls) from CFG</description>
    <requirements>
        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
    </requirements>
<stdio>
    <regex match="IOError" 
           source="both" 
           level="fatal" 
           description="IOError" />
    <regex match="UserWarning: gzip transfer encoding is experimental" 
           source="both" 
           level="warning" 
           description="Warning re use of gzip encoding" />
    <regex match="br.set_handle_gzip(True)" 
           source="both" 
           level="warning" 
           description="Warning re use of gzip encoding" />
    <regex match="IOError" 
           source="both" 
           level="fatal" 
           description="IOError" />
</stdio>


    <command interpreter="python"><![CDATA[  cfg_get_glycan_array_data.py -s "$species" -g "$glycanarrayversion" -i -j "$json_file" -o "$html_file" -d --filepath "xls_output" ]]></command>
    <inputs>
        <param name="species" type="select" label="Species"  >
            <option value="cTypeLectins" selected="true">cTypeLectins</option>
            <option value="iTypeLectins" selected="false">iTypeLectins</option>
            <option value="sTypeLectins" selected="false">sTypeLectins</option>
            <option value="otherAnimalLectins" selected="false">otherAnimalLectins</option>
            <option value="plantLectins" selected="false">plantLectins</option>
            <option value="antiBodies" selected="false">antiBodies</option>
            <option value="other" selected="false">other</option>
            <option value="cellsOrganisms" selected="false">cellsOrganisms</option>
            <option value="all" selected="false">all</option>
        </param>
        <param name="glycanarrayversion" type="select" label="Glycan Array Version">
            <option value="v1" selected="false">v1</option>
            <option value="v2" selected="false">v2</option>
            <option value="v3" selected="false">v3</option>
            <option value="pv1" selected="false">pv1</option>
            <option value="pv2" selected="false">pv2</option>
            <option value="pv21" selected="false">pv21</option>
            <option value="pv3" selected="false">pv3</option>
            <option value="pv31" selected="false">pv31</option>
            <option value="pv32" selected="false">pv32</option>
            <option value="pv4" selected="false">pv4</option>
            <option value="pv41" selected="false">pv41</option>
            <option value="pv42" selected="false">pv42</option>
            <option value="pv5" selected="false">pv5</option>
            <option value="pv51" selected="false">pv51</option>
            <option value="pv52" selected="false">pv52</option>
            <option value="bactv1" selected="false">bactv1</option>
            <option value="all" selected="true">all</option>

        </param>
    </inputs>
    <outputs>
        <data format="html" name="html_file" label="Summary_${tool.name}.html"/>
        <data format="txt" name="json_file" label="Summary_${tool.name}.json"/>
    </outputs>

    <help> <![CDATA[ 
.. class:: infomark

**What this tool does**

This tool download the metadata from the glycan array data available at the CFG.

.. class:: infomark

**Input**

Your choice of Species and Glycan Array Type.

----

.. class:: infomark

**Output**

HTML summary of retrieved information (Note links in html do not function within Galaxy).

JSON summary of glycan array metadata. 

xls data (not yet available in Galaxy) 


]]>
    </help>

</tool>