hicexplorer_hicplotmatrix: hicPlotMatrix.xml comparison

comparison hicPlotMatrix.xml @ 9:653c6fead9f9 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

author	iuc
date	Fri, 27 Apr 2018 03:36:47 -0400
parents	d398f5373c70
children	40b33e101621

comparison

equal deleted inserted replaced

-:d398f5373c70
+:653c6fead9f9
 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-<description>Plots a HiC matrix heatmap</description>
+<description>plot a Hi-C contact matrix heatmap</description>
 <macros>
 <token name="@BINARY@">hicPlotMatrix</token>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements" />
 ln -s $pca_conditional.pca_bigwig pca.bw &&
 #set $pca = '--bigwig pca.bw'
 #elif str($pca_conditional.pca_type) == '':
 #set $pca = ''
 #end if
 @BINARY@
 --matrix '$matrix_h5_cooler'
 #if $title and $title is not None:
 </command>
 <inputs>
 <expand macro='matrix_h5_cooler_macro' />
 <param argument="--title" type="text" optional="true" label="Plot title"/>
-<param argument="--scoreName" type="text" optional="true" label="Score name"/>
+<param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/>
 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
 label="Plot per chromosome"
 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
 label="Remove masked bins from the matrix"  />
 <param argument="--region" type="text" optional="True" label="Plot only this region"
 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless  --region2 is given"/>
 <param argument="--region2" type="text" optional="True" label="Region two to plot"
 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
-<param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
+<param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
-<param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/>
+<param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
 <expand macro="colormap" />
-<param argument="--vMin" type="float" optional="true" label="vMin"/>
+<param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
-<param argument="--vMax" type="float" optional="true" label="vMax"/>
+<param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>
 <conditional name="pca_conditional">
 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
 <option value='' selected="true"></option>
 <option value='bigwig'>bigwig</option>
 </param>
 <when value='' />
 <when value='bigwig'>
 <param name='pca_bigwig'  type="data" format="bigwig"
 label="Eigenvector file"/>
 </when>
 </conditional>
 <param name="image_file_format" type="select" label="Image output format">
 <option value="png" selected="True">png</option>
 <option value="svg">svg</option>
 </param>
 </inputs>
 <outputs>
-<data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
+<data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
 <change_format>
 <when input="image_file_format" value="svg" format="svg" />
 </change_format>
 </data>
 </outputs>
 <conditional name="pca_conditional">
 <param name="pca_type" value='bigwig'/>
 <param name="pca_bigwig" value="pca1.bw"/>
 </conditional>
 <param name='colormap' value='hot'/>
 <param name="image_file_format" value="svg" />
 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
 </test>
 </tests>
 <help><![CDATA[
 Contact matrix plot
 =======================
-``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other.
+**hicPlotMatrix** is a visualization tool for Hi-C contact matrices. It supports to plot genome-wide contact matrices, one or multiple chromosomes, a region or two regions against each other.
-Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
+Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
-Input
+_________________
+Usage
 -----
-Parameters
+This tool can be used on any h5 or cool Hi-C contact matrix. It is noteworthy that for comparisons of 2 matrices or more, they must all have the same or similar number of contacts.
-__________
-- the contact matrix: h5 or cool file format.
+_________________
-- A title for the plot
-- Score name
-- per chromosome
-- The chromosomes to include in the plot.
-- What to show:
-- The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
-- log / log1p of the values: It is recommended to use log1p.
-- Colormaps_ for the heatmap.
-- vMin / vMax
-- principal component: a bigwig file containing eigenvector information
 Output
 ------
-The contact matrix plotted for chromosome 1.
+**hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot:
-.. image:: SRR027956.svg
+.. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
-:width: 60%
+:width: 50%
+Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting.
-The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, `GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_.
+Another example is available below using Hi-C data published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``.
 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
 :width: 70 %
+_________________
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
 ]]></help>
 <expand macro="citations" />
 </tool>

Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 9:653c6fead9f9 draft