diff hicPCA.xml @ 2:97c797606746 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

--- a/hicPCA.xml	Tue Jan 02 10:19:28 2018 -0500
+++ b/hicPCA.xml	Wed Jan 03 13:32:31 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>computes the principal components for A / B compartment analysis</description>
     <macros>
         <token name="@BINARY@">hicPCA</token>
@@ -9,54 +9,51 @@
 
         hicPCA --matrix '$matrix_h5_cooler'
        
-        #if $outputFormat == 'bigwig'
-            --outputFileName 'pca1.bigwig' 'pca2.bigwig'
-            --format bigwig
-        #elif $outputFormat == 'bedgraph'
-            --outputFileName 'pca1.bedgraph' 'pca2.bedgraph'
-            --format bedgraph
-        #end if
+        --outputFileName pca1.$outputFormat pca2.$outputFormat
+        --format $outputFormat
+        
+        && mv pca1.$outputFormat pca1
+        && mv pca2.$outputFormat pca2
 
 ]]>
     </command>
     <inputs>
         <expand macro='matrix_h5_cooler_macro' />
         <param name='outputFormat' type='select' label="Output file format">
-            <option value='bigwig'>bigwig</option>
+            <option value='bigwig' selected="true">bigwig</option>
             <option value="bedgraph">bedgraph</option>
         </param>
 
     </inputs>
     <outputs>
        
-        <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig">
+        <data name="pca1" from_work_dir="pca1" format="bigwig">
             <filter>outputFormat == 'bigwig'</filter>
+            <change_format>
+                <when input="outputFormat" value="bedgraph" format="bedgraph" />
+            </change_format>
         </data>
-        <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig">
-            <filter>outputFormat == 'bigwig'</filter>
+        <data name="pca2" from_work_dir="pca2" format="bigwig">
+            <change_format>
+                <when input="outputFormat" value="bedgraph" format="bedgraph" />
+            </change_format>
         </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"/>
+            <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
+            <output name="pca2" 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"/>
+            <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
+            <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[