comparison macros.xml @ 1:76c040c8b9fc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3

0:6273e2721fa3

<macros>
    <token name="@WRAPPER_VERSION@">1.0.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.0.1">picrust</requirement>
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>

       </conditional>
    </xml>

    <xml name="biom_format_select">
        <param name="output_type" type="select" label="Format of the output BIOM file">
            <option value="json" selected="true">JSON</option>
            <option value="hdf5">HDF5</option>
            <option value="tsv">Classic (tab-separated text)</option>
        </param>
    </xml>

    <xml name="biom_output">
        <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
            <change_format>
                <when input="output_type" value="json" format="json"/>
                <when input="output_type" value="tsv" format="tabular"/>
                <when input="output_type" value="hdf5" format="hdf5"/>
            </change_format>
        </data>
    </xml>

    <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
        #if $output_type == "json":
            && biom convert -i tempbiom -o '$out_biom' --to-json
        #elif $output_type == "tsv":
            && biom convert -i tempbiom -o '$out_biom' --to-tsv
        #else
            && biom convert -i tempbiom -o '$out_biom' --to-hdf5
        #end if
    ]]></token>

    <token name="@PICRUST_OVERVIEW@">
<![CDATA[

marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.

For more information please visit:

- Picrust Documentation: https://picrust.github.io/picrust/
- Picrust GitHub: http://picrust.github.com/
- Picrust Support: https://groups.google.com/d/forum/picrust-users

**Reference Data**

Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/

]]>
    </token>

    <xml name="citations">

1:76c040c8b9fc

<macros>
    <token name="@WRAPPER_VERSION@">1.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.1.1">picrust</requirement>
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>

       </conditional>
    </xml>

    <xml name="biom_format_select">
        <param name="output_type" type="select" label="Format of the output BIOM file">
            <option value="hdf5" selected="true">HDF5</option>
            <option value="json">JSON</option>
            <option value="tsv">Classic (tab-separated text)</option>
        </param>
    </xml>

    <xml name="biom_format_select_no_json">
        <param name="output_type" type="select" label="Format of the output BIOM file">
            <option value="hdf5" selected="true">HDF5</option>
            <option value="tsv">Classic (tab-separated text)</option>
        </param>
    </xml>

    <xml name="biom_output">
        <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
            <change_format>
                <when input="output_type" value="json" format="biom1"/>
                <when input="output_type" value="tsv" format="tabular"/>
                <when input="output_type" value="hdf5" format="h5"/>
            </change_format>
        </data>
    </xml>

    <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
        #if $output_type == "hdf5":
            && mv tempbiom '$out_biom'
        #elif $output_type == "tsv":
            && biom convert -i tempbiom -o '$out_biom' --to-tsv
        #else:
            && biom convert -i tempbiom -o '$out_biom' --to-json
        #end if
    ]]></token>

    <token name="@PICRUST_OVERVIEW@">
<![CDATA[

marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.

For more information please visit:

- PICRUSt Documentation: https://picrust.github.io/picrust/
- PICRUSt GitHub: http://picrust.github.com/
- PICRUSt Support: https://groups.google.com/d/forum/picrust-users

**Reference Data**

Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/

]]>
    </token>

    <xml name="citations">