diff hicPlotMatrix.xml @ 4:fd5e51d2b558 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04

--- a/hicPlotMatrix.xml	Mon Nov 27 11:16:12 2017 -0500
+++ b/hicPlotMatrix.xml	Sat Dec 16 16:30:53 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>Plots a HiC matrix heatmap</description>
     <macros>
         <token name="@BINARY@">hicPlotMatrix</token>
@@ -26,7 +26,7 @@
             $perChromosome
             $clearMaskedBins
 
-            --whatToShow '$whatToShow.whatToShow_select'
+            --whatToShow heatmap
 
 
             ## special: --chromosomeOrder is optional, but if given needs at least one argument
@@ -57,11 +57,6 @@
                 --vMax $vMax
             #end if
 
-            #if $whatToShow.whatToShow_select != 'heatmap':
-                #if $whatToShow.zMax:
-                    --zMax $whatToShow.zMax
-                #end if
-            #end if
         && mv plot.$image_file_format plot
 ]]>
     </command>
@@ -75,21 +70,6 @@
         <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
             label="Remove masked bins from the matrix"  />
 
-        <conditional name="whatToShow">
-            <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
-                <option value="both">Show both</option>
-                <option value="heatmap" selected="true">Only heatmap</option>
-                <option value="3D">Only 3D</option>
-            </param>
-            <when value="both">
-                <expand macro="zMax" />
-            </when>
-            <when value="3D">
-                <expand macro="zMax" />
-            </when>
-            <when value="heatmap"/>
-        </conditional>
-
         <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
             help="This option overrides --region and --region2" >
             <param name="chromosome" type="text" >
@@ -102,7 +82,7 @@
         <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 *MINUS* log of the matrix values."/>
+        <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/>
 
         <expand macro="colormap" />
 
@@ -127,17 +107,55 @@
             <param name="region2" value="chrX:3100000-3600000"/>
             <param name="log1p" value="True"/>
             <param name="clearMaskedBins" value="True"/>
-            <param name="whatToShow_select" value="heatmap"/>
+            <!-- <param name="whatToShow_select" value="heatmap"/> -->
             <param name="image_file_format" value="png" />
             <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
+Contact matrix plot
+=======================
 
-**What it does**
+``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.
+
+Input
+-----
 
-Plots a Hi-C matrix heatmap.
+Parameters
+__________
+- the contact matrix
+- 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 bedgraph file 
 
+Output
+------
+
+The contact matrix plotted for chromosome 1.
+
+.. image:: SRR027956.svg
+   :width: 70%
+
+
+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>`_.
+
+.. 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>