diff hicAggregateContacts.xml @ 13:f0216498a666 draft

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

--- a/hicAggregateContacts.xml	Tue Jan 10 19:13:28 2023 +0000
+++ b/hicAggregateContacts.xml	Wed Oct 18 10:18:29 2023 +0000
@@ -66,7 +66,9 @@
     #if $vMax:
         --vMax $vMax
     #end if
-
+ 
+    $considerStrandDirection
+ 
     --outFileName plot.$image_file_format
     &&
     mv plot.$image_file_format plot
@@ -77,11 +79,11 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro="matrix_h5_cooler_macro" />
         <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
         <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />
 
-        <expand macro='range' />
+        <expand macro="range" />
         <param argument="--mode" type="select" label="Regions to consider.">
             <option value="inter-chr">inter-chr</option>
             <option value="intra-chr">intra-chr</option>
@@ -119,6 +121,7 @@
             <option value="mean">mean</option>
             <option value="sum">sum</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]." />
 
         <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 
                            a bin of the input matrix, by default only the first bin 
@@ -189,14 +192,14 @@
             <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
         <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
-            <filter>'outFileObsExp' in outputs</filter>
+            <filter>outputs == 'outFileObsExp'</filter>
             <change_format>
                 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
             </change_format>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
             <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
             <param name="numberOfBins" value="30" />