diff hicPlotMatrix.xml @ 9:653c6fead9f9 draft

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

--- a/hicPlotMatrix.xml	Wed Mar 07 03:44:12 2018 -0500
+++ b/hicPlotMatrix.xml	Fri Apr 27 03:36:47 2018 -0400
@@ -1,5 +1,5 @@
 <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>
@@ -13,7 +13,7 @@
         #elif str($pca_conditional.pca_type) == '':
             #set $pca = ''
         #end if
-        
+
         @BINARY@
 
             --matrix '$matrix_h5_cooler'
@@ -68,7 +68,7 @@
         <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" />
@@ -86,13 +86,13 @@
             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="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log 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. (log(Hi-C contacts))"/>
 
         <expand macro="colormap" />
 
-        <param argument="--vMin" type="float" optional="true" label="vMin"/>
-        <param argument="--vMax" type="float" optional="true" label="vMax"/>
+        <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" help="Maximum value of the plotted score."/>
 
         <conditional name="pca_conditional">
             <param name='pca_type' label='Datatype of eigenvector file' type='select'>
@@ -101,7 +101,7 @@
             </param>
             <when value='' />
             <when value='bigwig'>
-                <param name='pca_bigwig'  type="data" format="bigwig" 
+                <param name='pca_bigwig'  type="data" format="bigwig"
                             label="Eigenvector file"/>
             </when>
         </conditional>
@@ -111,7 +111,7 @@
         </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>
@@ -158,7 +158,7 @@
                 <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>
@@ -167,40 +167,35 @@
 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.
- Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
+**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.
+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
-__________
-- 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
+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.
+
+_________________
 
 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
-   :width: 60%
+.. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
+   :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
@@ -208,4 +203,3 @@
 ]]></help>
     <expand macro="citations" />
 </tool>
-