Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

diff hicCompareMatrices.xml @ 4:a37a9f34fe6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
author iuc
date Mon, 16 Dec 2019 22:36:51 +0000
parents 8650604f8ae7
children 693fb5e2638e
line wrap: on
line diff
--- a/hicCompareMatrices.xml	Mon Dec 16 13:15:09 2019 +0000
+++ b/hicCompareMatrices.xml	Mon Dec 16 22:36:51 2019 +0000
@@ -6,13 +6,16 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+    ln -s '$matrix1' 'matrix1.$matrix1.ext' &&
+    ln -s '$matrix2' 'matrix2.$matrix2.ext' &&
+
 
     @BINARY@
-    --matrices '$matrix1' '$matrix2'
+    --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
     --operation $operation
-    --outFileName matrix.$outputFormat
+    --outFileName 'matrix.$matrix1.ext'
 
-    && mv matrix.$outputFormat matrix
+    && mv 'matrix.$matrix1.ext' matrix
 ]]>
     </command>
     <inputs>
@@ -26,15 +29,11 @@
             <option value="ratio">ratio</option>
             <option value="log2ratio">log2ratio</option>
         </param>
-        <param name='outputFormat' type='select' label="Output file format">
-            <option value='h5'>HiCExplorer format</option>
-            <option value="cool">cool</option>
-        </param>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
+        <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
             <change_format>
-                <when input="outputFormat" value="cool" format="cool" />
+                <when input_dataset="matrix1" attribute="ext" value="h5" format="h5"/>
             </change_format>
         </data>
     </outputs>
@@ -43,15 +42,11 @@
             <param name="matrix1" value="small_test_matrix.h5"/>
             <param name="matrix2" value="small_test_matrix.h5"/>
             <param name="operation" value='log2ratio' />
-            <param name="outputFormat" value="h5" />
-            <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='10000'/>
-        </test>
-        <test>
-            <param name="matrix1" value="pearson_small_50kb.cool"/>
-            <param name="matrix2" value="pearson_small_50kb.cool"/>
-            <param name="operation" value='ratio' />
-            <param name="outputFormat" value="cool" />
-            <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
+            <output name="outFileName" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix'/>
+                </assert_contents>
+            </output>
         </test>
 
     </tests>