comparison biom_convert.xml @ 9:e177a8ea0bf1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4d77c1e4bd9f6876ee338858a8cd4c7e9528d54c

8:72ed72122deb

            <param name="type_selector" type="select" label="Choose the source BIOM format">
                <option value="tsv" selected="True">Tabular File</option>
                <option value="biom">BIOM File</option>
            </param>
            <when value="tsv">
                <param name="input_fp" argument="--input-fp" type="data" format="tabular" label="Input table" />
                <param name="process_obs_metadata" argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting">
                    <option value="" selected="True">Do Not process metadata</option>
                    <option value="taxonomy">taxonomy</option>
                    <option value="naive">naive</option>
                    <option value="sc_separated">sc_separated</option>
                </param>
            </when>
            <when value="biom">
                <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/>
            </when>
        </conditional>
        <conditional name="output">
            <param name="type_selector" type="select" label="Choose the output type">
                <option value="tsv">TSV-formatted (classic) table</option>
                <option value="biom" selected="True">BIOM</option>
            </param>
            <when value="tsv">
                <param name="header_key" argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" />
                <param name="output_metadata_id" argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" />
                <param name="tsv_metadata_formatter" argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" >
                    <option value="naive" selected="True">naive</option>
                    <option value="sc_separated">Semi-colon separated</option>
                </param>
            </when>
            <when value="biom">
                <param name="table_type" argument="--table-type" type="select" label="Table Type" >
                    <option value="OTU table">OTU table</option>
                    <option value="Pathway table">Pathway table</option>
                    <option value="Function table">Function table</option>
                    <option value="Ortholog table">Ortholog table</option>
                    <option value="Gene table">Gene table</option>

                        <option value="hdf5">HDF5-formatted table (BIOM2)</option>
                    </param>
                    <when value="json">
                    </when>
                    <when value="hdf5">
                        <param name="collapsed_observations" argument="--collapsed-observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples"/>
                        <param name="collapsed_samples" argument="--collapsed-samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/>
                    </when>
                </conditional>
                <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />
                <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="biom1" name="output_fp">

9:e177a8ea0bf1

            <param name="type_selector" type="select" label="Choose the source BIOM format">
                <option value="tsv" selected="True">Tabular File</option>
                <option value="biom">BIOM File</option>
            </param>
            <when value="tsv">
                <param argument="--input-fp" type="data" format="tabular" label="Input table" />
                <param argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting">
                    <option value="" selected="True">Do Not process metadata</option>
                    <option value="taxonomy">taxonomy</option>
                    <option value="naive">naive</option>
                    <option value="sc_separated">sc_separated</option>
                </param>
            </when>
            <when value="biom">
                <param argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/>
            </when>
        </conditional>
        <conditional name="output">
            <param name="type_selector" type="select" label="Choose the output type">
                <option value="tsv">TSV-formatted (classic) table</option>
                <option value="biom" selected="True">BIOM</option>
            </param>
            <when value="tsv">
                <param argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" />
                <param argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" />
                <param argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" >
                    <option value="naive" selected="True">naive</option>
                    <option value="sc_separated">Semi-colon separated</option>
                </param>
            </when>
            <when value="biom">
                <param argument="--table-type" type="select" label="Table Type" >
                    <option value="OTU table">OTU table</option>
                    <option value="Pathway table">Pathway table</option>
                    <option value="Function table">Function table</option>
                    <option value="Ortholog table">Ortholog table</option>
                    <option value="Gene table">Gene table</option>

                        <option value="hdf5">HDF5-formatted table (BIOM2)</option>
                    </param>
                    <when value="json">
                    </when>
                    <when value="hdf5">
                        <param argument="--collapsed-observations" type="boolean" truevalue="--collapsed-observations" falsevalue="" checked="False" label="Use collapsed observations"/>
                        <param argument="--collapsed-samples" type="boolean" truevalue="--collapsed-samples" falsevalue="" checked="False" label="Use collapsed samples"/>
                    </when>
                </conditional>
                <param argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />
                <param argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="biom1" name="output_fp">