diff hicPlotViewpoint.xml @ 0:58d146c74d72 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotViewpoint.xml	Sat Dec 30 09:11:56 2017 -0500
@@ -0,0 +1,88 @@
+<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>computes the principal components for A / B compartment analysis</description>
+    <macros>
+        <token name="@BINARY@">hicPlotViewpoint</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        hicPlotViewpoint --matrix '$matrix_h5_cooler'
+        #if $interactionOutFileName:
+            $interactionOutFileName interactions.bedgraph
+        #end if
+        --outFileName plot.$image_file_format
+        --region $region
+        --referencePoint $referencePoint
+        && mv plot.$image_file_format plot
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <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">
+            <option value="png">png</option>
+            <option value="svg">svg</option>
+        </param>
+
+    </inputs>
+    <outputs>
+       
+        <data format="png" name="outFileName" from_work_dir="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'>
+            <filter>interactionOutFileName</filter>
+        </data>
+        
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="image_file_format" value="png" />
+            <param name='region' value='X:3000000-3500000' />
+            <param name='referencePoint' value='X:3200000' />
+            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="image_file_format" value="png" />
+            <param name='region' value='X:3000000-3500000' />
+            <param name='referencePoint' value='X:3200000-3300000' />
+            <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.
+
+Input
+-----
+- the matrix to be analysed
+
+Parameters
+__________
+- Output file format: bigwig or bedgraph
+
+Output
+------
+Two files with the first and the second eigenvector.
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>