diff hicPlotViewpoint.xml @ 3:745e77f4e81e draft

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

--- a/hicPlotViewpoint.xml	Wed Mar 07 03:41:30 2018 -0500
+++ b/hicPlotViewpoint.xml	Fri Apr 27 03:35:16 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>computes the principal components for A / B compartment analysis</description>
+    <description>plot interactions around a viewpoint</description>
     <macros>
         <token name="@BINARY@">hicPlotViewpoint</token>
         <import>macros.xml</import>
@@ -22,7 +22,7 @@
         <expand macro="region" />
         <param name="referencePoint" type="text" label="Reference point"
             help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
-   
+
         <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
                             label="Create bedgraph file with interactions" />
         <param name="image_file_format" type="select" label="Image output format">
@@ -32,17 +32,17 @@
 
     </inputs>
     <outputs>
-       
-        <data format="png" name="outFileName" from_work_dir="plot">
+
+        <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="png" format="png" />
                 <when input="image_file_format" value="svg" format="svg" />
             </change_format>
         </data>
-        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'>
+        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
             <filter>interactionOutFileName</filter>
         </data>
-        
+
     </outputs>
     <tests>
         <test>
@@ -60,25 +60,34 @@
             <param name='interactionOutFileName' value='True' />
             <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
             <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
-            
+
         </test>
     </tests>
     <help><![CDATA[
-Principal component analysis
-============================
-`hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.
+Plot Viewpoint
+==============
 
-Input
+**hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data.
+This plotting method allows to make long-range interactions more visible.
+
+_________________
+
+Usage
 -----
-- the matrix to be analysed
 
-Parameters
-__________
-- Output file format: bigwig or bedgraph
+This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.
+
+_________________
 
 Output
 ------
-Two files with the first and the second eigenvector.
+
+**hicPlotViewpoint** outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.
+
+.. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
+   :width: 80 %
+
+_________________
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_