comparison deepTools_macros.xml @ 9:6531acf8209f draft

"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

8:0741d8c3bf35

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.3.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.3.0">deeptools</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

                            If more specific clustering methods are required it is advisable to save the underlying matrix and
                            run the clustering using other software."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />
        </conditional>
    </xml>

            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
                #end if
            #end if
        #end if
    </token>

    <xml name="samFlags">
        <param argument="--samFlagInclude" type="integer" optional="True" value=""

        <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
            label="Use a metagene model"
            help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
        <param argument="--transcriptID" optional="True" value="transcript" type="text"
            label="transcript designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
        <param argument="--exonID" optional="True" value="exon" type="text"
            label="exon designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
            label="transcriptID key designator"
            help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
                  or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
                  as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be

.. class:: infomark

For more information on the tools, please visit our `help site`_.

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://deeptools.readthedocs.org/

    </token>

            <option value="bwr">bwr</option>
            <option value="hsv">hsv</option>
            <option value="brg">brg</option>
            <option value="jet">jet</option>
            <option value="afmhot">afmhot</option>
            <option value="Accent_r">Accent reversed</option>
            <option value="Spectral_r">Spectral reversed</option>
            <option value="Set1_r">Set1 reversed</option>
            <option value="Set2_r">Set2 reversed</option>
            <option value="Set3_r">Set3 reversed</option>

            <option value="bwr_r">bwr reversed</option>
            <option value="hsv_r">hsv reversed</option>
            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
        </param>

    </xml>

</macros>

9:6531acf8209f

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.3.2.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.3.2">deeptools</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

                            If more specific clustering methods are required it is advisable to save the underlying matrix and
                            run the clustering using other software."/>
                    </when>
                    <when value="none" />
                </conditional>
                <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
                    label="Compute the silhouette score for each region"
                    help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
                    The silhouette score is a measure of how similar a region is to other regions in the same cluster as
                    opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
                    The silhouette evaluation can be very slow when you have more than 100 000 regions." />
            </when>
            <when value="yes" />
        </conditional>
    </xml>

            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
                #end if
            #end if
            $advancedOpt.used_multiple_regions.silhouette
        #end if
    </token>

    <xml name="samFlags">
        <param argument="--samFlagInclude" type="integer" optional="True" value=""

        <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
            label="Use a metagene model"
            help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
        <param argument="--transcriptID" optional="True" value="transcript" type="text"
            label="transcript designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
        <param argument="--exonID" optional="True" value="exon" type="text"
            label="exon designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
            label="transcriptID key designator"
            help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
                  or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
                  as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be

.. class:: infomark

For more information on the tools, please visit our `help site`_.

For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

.. _Biostars: http://biostars.org
.. _on github: http://github.com
.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://deeptools.readthedocs.org/

    </token>

            <option value="bwr">bwr</option>
            <option value="hsv">hsv</option>
            <option value="brg">brg</option>
            <option value="jet">jet</option>
            <option value="afmhot">afmhot</option>
            <option value="Wistia">Wistia</option>
            <option value="cividis">cividis</option>
            <option value="icefire">icefire</option>
            <option value="inferno">inferno</option>
            <option value="magma">magma</option>
            <option value="mako">mako</option>
            <option value="nipy_spectral">nipy_spectral</option>
            <option value="plasma">plasma</option>
            <option value="rocket">rocket</option>
            <option value="tab10">tab10</option>
            <option value="tab20">tab20</option>
            <option value="tab20b">tab20b</option>
            <option value="tab20c">tab20c</option>
            <option value="twilight">twilight</option>
            <option value="twilight_shifted">twilight_shifted</option>
            <option value="viridis">viridis</option>
            <option value="vlag">vlag</option>
            <option value="Accent_r">Accent reversed</option>
            <option value="Spectral_r">Spectral reversed</option>
            <option value="Set1_r">Set1 reversed</option>
            <option value="Set2_r">Set2 reversed</option>
            <option value="Set3_r">Set3 reversed</option>

            <option value="bwr_r">bwr reversed</option>
            <option value="hsv_r">hsv reversed</option>
            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
            <option value="Wistia_r">Wistia reversed</option>
            <option value="cividis_r">cividis reversed</option>
            <option value="icefire_r">icefire reversed</option>
            <option value="inferno_r">inferno reversed</option>
            <option value="magma_r">magma reversed</option>
            <option value="mako_r">mako reversed</option>
            <option value="nipy_spectral_r">nipy_spectral reversed</option>
            <option value="plasma_r">plasma reversed</option>
            <option value="rocket_r">rocket reversed</option>
            <option value="tab10_r">tab10 reversed</option>
            <option value="tab20_r">tab20 reversed</option>
            <option value="tab20b_r">tab20b reversed</option>
            <option value="tab20c_r">tab20c reversed</option>
            <option value="twilight_r">twilight reversed</option>
            <option value="twilight_shifted_r">twilight_shifted reversed</option>
            <option value="viridis_r">viridis reversed</option>
            <option value="vlag_r">vlag reversed</option>
        </param>

    </xml>

</macros>