diff hicPCA.xml @ 0:61165fbb020d 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/hicPCA.xml	Sat Dec 30 09:14:06 2017 -0500
@@ -0,0 +1,84 @@
+<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>computes the principal components for A / B compartment analysis</description>
+    <macros>
+        <token name="@BINARY@">hicPCA</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        hicPCA --matrix '$matrix_h5_cooler'
+       
+        #if $outputFormat == 'bigwig'
+            --outputFileName 'pca1.bigwig' 'pca2.bigwig'
+            --format bigwig
+        #elif $outputFormat == 'bedgraph'
+            --outputFileName 'pca1.bedgraph' 'pca2.bedgraph'
+            --format bedgraph
+        #end if
+
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='bigwig'>bigwig</option>
+            <option value="bedgraph">bedgraph</option>
+        </param>
+
+    </inputs>
+    <outputs>
+       
+        <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig">
+            <filter>outputFormat == 'bigwig'</filter>
+        </data>
+        <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig">
+            <filter>outputFormat == 'bigwig'</filter>
+        </data>
+
+        <data name="pca1_bedgraph" from_work_dir="pca1.bedgraph" format="bedgraph">
+            <filter>outputFormat == 'bedgraph'</filter>
+        </data>
+        <data name="pca2_bedgraph" from_work_dir="pca2.bedgraph" format="bedgraph">
+            <filter>outputFormat == 'bedgraph'</filter>
+        </data>
+        
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+            <param name="outputFormat" value="bedgraph" />
+            <output name="pca1_bedgraph" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
+            <output name="pca2_bedgraph" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+
+            <param name="outputFormat" value="bigwig" />
+            <output name="pca1_bw" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
+            <output name="pca2_bw" file="pca2.bw" ftype="bigwig" 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>