diff hicAdjustMatrix.xml @ 8:2dccb6bb0add draft

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

--- a/hicAdjustMatrix.xml	Tue Jan 10 19:05:09 2023 +0000
+++ b/hicAdjustMatrix.xml	Wed Oct 18 10:42:59 2023 +0000
@@ -25,11 +25,15 @@
             --regions '$chromosomeOrRegionFile_conditional.regions'
         #end if
 
+        #if not $interIntra_selector == 'keep':
+            --interIntraHandling $interIntra_selector
+        #end if
         && mv '$matrix_file_out' matrix
+
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro="matrix_h5_cooler_macro" />
         <param name="action_selector" type="select" label="Apply action">
             <option value="keep" selected="True">keep</option>
             <option value="remove">remove</option>
@@ -51,6 +55,11 @@
                 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
             </when>
         </conditional>
+        <param name="interIntra_selector" type="select" label="Remove inter- or intra chromosomal regions">
+            <option value="keep" selected="True">Do not apply</option>
+            <option value="inter">Remove inter-chromosomal contacts</option>
+            <option value="intra">Remove intra-chromosomal contacts</option>
+        </param>
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="matrix" format="h5">
@@ -64,15 +73,15 @@
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="action_selector" value="keep" />
             <conditional name="chromosomeOrRegionFile_conditional">
-                <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' />
+                <param name="chromosomeOrRegionFile_selector" value="optionChromosomes" />
                 <repeat name="chromosomeOrder">
-                    <param name="chromosome" value='chrX' />
-                    <param name="chromosome" value='chr3R' />
+                    <param name="chromosome" value="chrX" />
+                    <param name="chromosome" value="chr3R" />
                 </repeat>
             </conditional>
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix' />
+                    <has_h5_keys keys="intervals,matrix" />
                 </assert_contents>
             </output>
         </test>
@@ -80,12 +89,12 @@
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <param name="action_selector" value="mask" />
             <conditional name="chromosomeOrRegionFile_conditional">
-                <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' />
-                <param name="regions" value='regions.bed' />
+                <param name="chromosomeOrRegionFile_selector" value="optionRegionFile" />
+                <param name="regions" value="regions.bed" />
             </conditional>
             <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>