# HG changeset patch
# User iuc
# Date 1673545256 0
# Node ID 608538d083a2a358d21e30307f2813efc27647ce
# Parent  c852ad97ba280f243cac7178567578d9f1f34983
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02

diff -r c852ad97ba28 -r 608538d083a2 hicDifferentialTAD.xml
--- a/hicDifferentialTAD.xml	Tue Mar 16 21:17:26 2021 +0000
+++ b/hicDifferentialTAD.xml	Thu Jan 12 17:40:56 2023 +0000
@@ -61,7 +61,8 @@
             <param name="mode_selector" value="all" />
             <param name="modeReject" value="one" />
             <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" />
-            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" />
+            <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes-->
+            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r c852ad97ba28 -r 608538d083a2 macros.xml
--- a/macros.xml	Tue Mar 16 21:17:26 2021 +0000
+++ b/macros.xml	Thu Jan 12 17:40:56 2023 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
     <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -333,7 +333,7 @@
         <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
     </xml>
     <xml name="xMax">
-        <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
+        <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
     </xml>
     <xml name="filterThreshold">
         <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />