diff hicMergeMatrixBins.xml @ 21:08a76d7a4bdb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

--- a/hicMergeMatrixBins.xml	Tue Jan 10 17:51:49 2023 +0000
+++ b/hicMergeMatrixBins.xml	Mon Jul 01 19:22:14 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
     <macros>
         <token name="@BINARY@">hicMergeMatrixBins</token>
@@ -11,12 +11,12 @@
             --matrix 'matrix.$matrix_h5_cooler.ext'
             --numBins $numBins
             $runningWindow
-            --outFileName 'matrix.$matrix_h5_cooler.ext'
-        && mv 'matrix.$matrix_h5_cooler.ext' matrix
+            --outFileName 'out_matrix.$matrix_h5_cooler.ext'
+        && mv 'out_matrix.$matrix_h5_cooler.ext' matrix
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro="matrix_h5_cooler_macro" />
         <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
         <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
     </inputs>
@@ -33,7 +33,7 @@
             <param name="numBins" value="5" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix,nan_bins' />
+                    <has_h5_keys keys="intervals,matrix,nan_bins" />
                 </assert_contents>
             </output>
         </test>