diff hicAverageRegions.xml @ 8:c72fa6cb8817 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicAverageRegions.xml	Tue Jan 10 19:09:18 2023 +0000
+++ b/hicAverageRegions.xml	Wed Oct 18 11:10:09 2023 +0000
@@ -17,13 +17,14 @@
             --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
         #end if
         --coordinatesToBinMapping $coordinatesToBinMapping_selector
+        $considerStrandDirection
         --outFileName output_matrix.npz
 
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
-        <param argument="--regions" type="data" format='bed' label="Regions to average" help="BED file which stores a list of regions that are summed and averaged." />
+        <expand macro="matrix_h5_cooler_macro" />
+        <param argument="--regions" type="data" format="bed" label="Regions to average" help="BED file which stores a list of regions that are summed and averaged." />
 
         <conditional name="rangeFormat_conditional">
             <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
@@ -44,6 +45,8 @@
             <option value="center" selected="True">Center</option>
             <option value="end" selected="True">End</option>
         </param>
+        <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />
+
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" />
@@ -53,21 +56,21 @@
             <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
             <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed"/>
             <conditional name="rangeFormat_conditional">
-                <param name="rangeFormat_selector" value='optionGenomicUnits' />
-                <param name="upstreamRange" value='100000' />
-                <param name="downstreamRange" value='100000' />
+                <param name="rangeFormat_selector" value="optionGenomicUnits" />
+                <param name="upstreamRange" value="100000" />
+                <param name="downstreamRange" value="100000" />
             </conditional>
-            <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" />
+            <output name="outFileName" file="hicAverageRegions/result_range_100000.npz" ftype="zip" compare="sim_size" delta="20000" />
         </test>
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
             <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed" />
             <conditional name="rangeFormat_conditional">
-                <param name="rangeFormat_selector" value='optionBinUnits' />
-                <param name="upstreamRange" value='100' />
-                <param name="downstreamRange" value='100' />
+                <param name="rangeFormat_selector" value="optionBinUnits" />
+                <param name="upstreamRange" value="100" />
+                <param name="downstreamRange" value="100" />
             </conditional>
-            <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" />
+            <output name="outFileName" file="hicAverageRegions/result_rangeInBins_100.npz" ftype="zip" compare="sim_size" delta="20000" />
         </test>
     </tests>
     <help><![CDATA[