comparison heatmapper.xml @ 10:a68a771625d2 draft

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9:73761f33f198

<tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
  <description>creates a heatmap for a score associated to genomic regions</description>

  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
    <requirement type="package" version="1.2.1">matplotlib</requirement>
    <requirement type="package" version="0.12.0">scipy</requirement>
    <requirement type="package" version="0.1">ucsc_tools</requirement>
    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
    <requirement type="package" >deepTools</requirement>
  </requirements>

  <command>
  heatmapper

  --matrixFile $matrixFile
  #if $output.showOutputSettings == "yes"

  ; mv $newoutFileName $outFileName
  </command>
  <inputs>
    <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
    <conditional name="output" >
        <param name="showOutputSettings" type="select" label="Show advanced output settings" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>
      </param>
      <when value="no" />
      <when value="yes">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
        <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
        <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
        <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
    </when>
    </conditional>

    <conditional name="advancedOpt" >
      <param name="showAdvancedOpt" type="select" label="Show advanced options" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>

          <option value="std">std</option>
        </param>

        <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />

        <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu" selected="true">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>
            <option value="Set2">Set2</option>
            <option value="Set3">Set3</option>
            <option value="Dark2">Dark2</option>
            <option value="Reds">Reds</option>
            <option value="Oranges">Oranges</option>
            <option value="Greens">Greens</option>
            <option value="Blues">Blues</option>
            <option value="Greys">Greys</option>
            <option value="Purples">Purples</option>
            <option value="Paired">Paired</option>
            <option value="Pastel1">Pastel1</option>
            <option value="Pastel2">Pastel2</option>
            <option value="spring">spring</option>
            <option value="summer">summer</option>
            <option value="autumn">autumn</option>
            <option value="winter">winter</option>
            <option value="hot">hot</option>
            <option value="coolwarm">coolwarm</option>
            <option value="cool">cool</option>
            <option value="seismic">seismic</option>
            <option value="terrain">terrain</option>
            <option value="ocean">ocean</option>
            <option value="rainbow">rainbow</option>
            <option value="bone">bone</option>
            <option value="flag">flag</option>
            <option value="prism">prism</option>
            <option value="cubehelix">cubehelix</option>
            <option value="binary">binary</option>
            <option value="pink">pink</option>
            <option value="gray">gray</option>
            <option value="copper">copper</option>
            <option value="BrBG">BrBG</option>
            <option value="BuGn">BuGn</option>
            <option value="BuPu">BuPu</option>
            <option value="GnBu">GnBu</option>
            <option value="OrRd">OrRd</option>
            <option value="PiYG">PiYG</option>
            <option value="PRGn">PRGn</option>
            <option value="PuOr">PuOr</option>
            <option value="PuRd">PuRd</option>
            <option value="PuBu">PuBu</option>
            <option value="RdBu">RdBu</option>
            <option value="RdGy">RdGy</option>
            <option value="RdPu">RdPu</option>
            <option value="YlGn">YlGn</option>
            <option value="PuBuGn">PuBuGn</option>
            <option value="RdYlGn">RdYlGn</option>
            <option value="YlGnBu">YlGnBu</option>
            <option value="YlOrBr">YlOrBr</option>
            <option value="YlOrRd">YlOrRd</option>
            <option value="gist_gray">gist_gray</option>
            <option value="gist_stern">gist_stern</option>
            <option value="gist_earth">gist_earth</option>
            <option value="gist_yarg">gist_yarg</option>
            <option value="gist_ncar">gist_ncar</option>
            <option value="gist_rainbow">gist_rainbow</option>
            <option value="gist_heat">gist_heat</option>
            <option value="gnuplot">gnuplot</option>
            <option value="gnuplot2">gnuplot2</option>
            <option value="CMRmap">CMRmap</option>
            <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="Dark2_r">Dark2 reversed</option>
            <option value="Reds_r">Reds reversed</option>
            <option value="Oranges_r">Oranges reversed</option>
            <option value="Greens_r">Greens reversed</option>
            <option value="Blues_r">Blues reversed</option>
            <option value="Greys_r">Greys reversed</option>
            <option value="Purples_r">Purples reversed</option>
            <option value="Paired_r">Paired reversed</option>
            <option value="Pastel1_r">Pastel1 reversed</option>
            <option value="Pastel2_r">Pastel2 reversed</option>
            <option value="spring_r">spring reversed</option>
            <option value="summer_r">summer reversed</option>
            <option value="autumn_r">autumn reversed</option>
            <option value="winter_r">winter reversed</option>
            <option value="hot_r">hot reversed</option>
            <option value="coolwarm_r">coolwarm reversed</option>
            <option value="cool_r">cool reversed</option>
            <option value="seismic_r">seismic reversed</option>
            <option value="terrain_r">terrain reversed</option>
            <option value="ocean_r">ocean reversed</option>
            <option value="rainbow_r">rainbow reversed</option>
            <option value="bone_r">bone reversed</option>
            <option value="flag_r">flag reversed</option>
            <option value="prism_r">prism reversed</option>
            <option value="cubehelix_r">cubehelix reversed</option>
            <option value="binary_r">binary reversed</option>
            <option value="pink_r">pink reversed</option>
            <option value="gray_r">gray reversed</option>
            <option value="copper_r">copper reversed</option>
            <option value="BrBG_r">BrBG reversed</option>
            <option value="BuGn_r">BuGn reversed</option>
            <option value="BuPu_r">BuPu reversed</option>
            <option value="GnBu_r">GnBu reversed</option>
            <option value="OrRd_r">OrRd reversed</option>
            <option value="PiYG_r">PiYG reversed</option>
            <option value="PRGn_r">PRGn reversed</option>
            <option value="PuOr_r">PuOr reversed</option>
            <option value="PuRd_r">PuRd reversed</option>
            <option value="PuBu_r">PuBu reversed</option>
            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="YlGn_r">YlGn reversed</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="RdYlBu_r">RdYlBu reversed</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="gist_gray_r">gist_gray reversed</option>
            <option value="gist_stern_r">gist_stern reversed</option>
            <option value="gist_earth_r">gist_earth reversed</option>
            <option value="gist_yarg_r">gist_yarg reversed</option>
            <option value="gist_ncar_r">gist_ncar reversed</option>
            <option value="gist_rainbow_r">gist_rainbow reversed</option>
            <option value="gist_heat_r">gist_heat reversed</option>
            <option value="gnuplot_r">gnuplot reversed</option>
            <option value="gnuplot2_r">gnuplot2 reversed</option>
            <option value="CMRmap_r">CMRmap 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>

        <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
        <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
        <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
        <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>

    </tests>
  <help>

**What it does**

The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; it can also be generated separately by the tool profiler). We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, e.g. one plot per chromosome, simply supply each group as an individual BED file.

-----

.. class:: infomark

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://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de

  </help>
</tool>

10:a68a771625d2

<tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
    <description>creates a heatmap for a score associated to genomic regions</description>
    <expand macro="requirements">
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.7.1">numpy</requirement>
        <requirement type="package" version="1.2.1">matplotlib</requirement>
        <requirement type="package" version="0.12.0">scipy</requirement>
    </expand>
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
  <command>
  heatmapper

  --matrixFile $matrixFile
  #if $output.showOutputSettings == "yes"

  ; mv $newoutFileName $outFileName
  </command>
  <inputs>
    <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>

    <expand macro="graphic_output_settings" />

    <conditional name="advancedOpt" >
      <param name="showAdvancedOpt" type="select" label="Show advanced options" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>

          <option value="std">std</option>
        </param>

        <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />

        <expand macro="colormap" />

        <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
        <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
        <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
        <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>

    </tests>
  <help>

**What it does**

The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. 
Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. 
In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; 
it can also be generated separately by the tool profiler). 
We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as 
with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, 
e.g. one plot per chromosome, simply supply each group as an individual BED file.


.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
   :alt: Heatmap of RNA Polymerase II ChIP-seq


-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>