comparison computeMatrix.xml @ 13:e68acded4691 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11

12:a2c1268c8dec

    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        #import tempfile

        @BINARY@

            $mode.mode_select
            --regionsFileName
            #for $rf in $regionsFiles:
                '$rf.regionsFile' 
            #end for
            --scoreFileName
            #for $bw in $scoreFileName:
                '$bw' 
            #end for
            --outFileName '$outFileName'

            @THREADS@

            #if $output.showOutputSettings == "yes"

            #if $advancedOpt.showAdvancedOpt == "yes":
                --sortRegions '$advancedOpt.sortRegions'
                --sortUsing '$advancedOpt.sortUsing'
                --averageTypeBins '$advancedOpt.averageTypeBins'
                $advancedOpt.skipNAs
                $advancedOpt.skipZeros
                --binSize $advancedOpt.binSize

                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
                    --minThreshold $advancedOpt.minThreshold
                #end if

                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <param name="scoreFileName" format="bigwig" type="data"
            label="Score file" multiple="True"
            help="You can generate a bigWig file from either a
            bedGraph or WIG file using UCSC tools or from a BAM file using the
            bamCoverage tool. (--scoreFileName)"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are
                stretched or shrunk to the same length (in bases) that is indicated
                by the user. Reference-point refers to a position within the BED
                regions (e.g start of region). In the reference-point mode only
                those genomic positions before (upstream) and/or after (downstream)
                the reference point will be considered.">
                <option value="scale-regions" selected="true">scale-regions</option>
                <option value="reference-point">reference-point</option>
            </param>

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

                <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
                    label="Convert missing values to 0?."
                    help="If set to 'yes', missing values (NAs) are converted to 0.
                          The default is to ignore such cases, which will be
                          depicted as black areas once a heatmap is created." />

                <expand macro="skipZeros" />
                <expand macro="skipNAs" />

                <param name="minThreshold" type="float" optional="True"
                    label="Minimum threshold"
                    help="Any region containing a value that is equal or less than this numeric
                    value will be skipped. This is useful to skip, for example, genes where the
                    read count is zero for any of the bins. This could be the result of
                    unmappable areas and can bias the overall results. (--minThreshold)"/>
                <param name="maxThreshold" type="float" optional="True"
                    label="Maximum threshold"
                    help="Any region containing a value that is equal or higher that this
                    numeric value will be skipped. The max threshold is useful to skip those

            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="sortUsing" value="sum" />
            <param name="averageTypeBins" value="sum" />
            <param name="skipNAs" value="False" />
            <param name="beforeRegionStartLength" value="10" />
            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>

            <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
    </tests>
  <help>
<![CDATA[
**What it does**

This tool prepares an intermediate file (a gzipped table of values)
that contains scores associated with genomic regions and can be used
afterwards to plot a heatmap or profile.

Genomic regions can really be anything - genes, parts of genes, ChIP-seq
peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. If you would like to compare different groups of regions
(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.

computeMatrix can also be used to filter and sort
regions according to their score by making use of its advanced output options.


.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
   :alt: Relationship between computeMatrix, heatmapper and profiler


You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html


-----

@REFERENCES@
]]>

13:e68acded4691

    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        #import tempfile
        #set bw_files=[]
        #for $counter, $bigwig in enumerate($scoreFileName):
            ln -s "${bigwig}" "file_${counter}.bw" &&
            #silent $bw_files.append('file_%s.bw' % $counter)
        #end for

        #set bed_files=[]
        #for $counter, $rf in enumerate($regionsFiles):
            ln -s "${rf.regionsFile}" "group_${counter}.bed" &&
            #silent $bed_files.append('group_%s.bed' % $counter)
        #end for

        @BINARY@

            $mode.mode_select
            --regionsFileName '#echo "' '".join($bed_files)#'

            --scoreFileName '#echo "' '".join($bw_files)#'

            --outFileName '$outFileName'

            @THREADS@

            #if $output.showOutputSettings == "yes"

            #if $advancedOpt.showAdvancedOpt == "yes":
                --sortRegions '$advancedOpt.sortRegions'
                --sortUsing '$advancedOpt.sortUsing'
                --averageTypeBins '$advancedOpt.averageTypeBins'
                $advancedOpt.skipZeros
                $advancedOpt.missingDataAsZero
                --binSize $advancedOpt.binSize

                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
                    --minThreshold $advancedOpt.minThreshold
                #end if

                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <param name="scoreFileName" format="bigwig" type="data"
            label="Score file" multiple="True"
            help="You can generate a bigWig file from a BAM file using the
            bamCoverage tool. (--scoreFileName)"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are
                stretched or shrunken to the same length (in bases) that is indicated
                by the user. Reference-point refers to a position within the BED
                regions (start or end of each region). In the reference-point mode only
                those genomic positions before (upstream) and/or after (downstream)
                the reference point will be considered.">
                <option value="scale-regions" selected="true">scale-regions</option>
                <option value="reference-point">reference-point</option>
            </param>

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

                <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
                    label="Convert missing values to 0?"
                    help="If set to 'yes', missing values (NAs) are converted
                     to 0. If you want to use clustering with plotHeatmap
                     or plotProfile, set this to 'yes'.
                          The default is to ignore missing values, which will be
                          depicted as black areas once a heatmap is created.
                           (--missingDataAsZero)" />

                <expand macro="skipZeros" />

                <param name="minThreshold" type="float" optional="True"
                    label="Minimum threshold"
                    help="Any region containing a value that is equal or less than this numeric
                    value will be skipped. This is useful to skip, for example, genes where the
                    read count is zero for any of the bins which could be the result of
                    unmappable areas and can bias the overall results. (--minThreshold)"/>
                <param name="maxThreshold" type="float" optional="True"
                    label="Maximum threshold"
                    help="Any region containing a value that is equal or higher that this
                    numeric value will be skipped. The max threshold is useful to skip those

            <param name="showAdvancedOpt" value="yes" />
            <param name="mode_select" value="reference-point" />
            <param name="binSize" value="10" />
            <param name="sortUsing" value="sum" />
            <param name="averageTypeBins" value="sum" />
            <param name="beforeRegionStartLength" value="10" />
            <param name="afterRegionStartLength" value="10" />
            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
        <test>

            <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
        </test>
    </tests>
  <help>
<![CDATA[

What it does
----------------

This tool prepares an intermediate file (a gzipped table of values)
that contains scores associated with genomic regions.
The regions can either be scaled to the same size (using the ``scale-regions`` mode) or you can choose the start, end, or center of each region as the focus point for the score calculations.
For more details, check out the explanation `here <file:///Users/frd2007/Documents/MPI/deepTools/docs/_build/html/content/tools/computeMatrix.html#details>`_.

The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``.
See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots.

.. image:: $PATH_TO_IMAGES/computeMatrix_overview.png
   :alt: Relationship between computeMatrix, heatmapper and profiler
   :width: 600
   :height: 418

=======

Usage hints
-------------

The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions".

.. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png
   :width: 600
   :height: 150

You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest.

.. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png
   :width: 600
   :height: 136

The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often:

* ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it.
* ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap.
* ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'.


Output files
---------------

The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``.

The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**.

**TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings".

.. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png
   :width: 600
   :height: 189

.. image:: $PATH_TO_IMAGES/computeMatrix_output.png
   :width: 600
   :height: 297

Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too.

See the following table for the optional output options:

+-----------------------------------+--------------------+-----------------+-----------------+
|  **optional output type**         |  **computeMatrix** | **plotHeatmap** | **plotProfile** |
+-----------------------------------+--------------------+-----------------+-----------------+
| values underlying the heatmap     |  yes               | yes             | no              |
+-----------------------------------+--------------------+-----------------+-----------------+
| values underlying the profile     | no                 | no              | yes             |
+-----------------------------------+--------------------+-----------------+-----------------+
| sorted and/or filtered regions    | yes                | yes             | yes             |
+-----------------------------------+--------------------+-----------------+-----------------+

**More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.

-----

@REFERENCES@
]]>