# HG changeset patch
# User iuc
# Date 1730760861 0
# Node ID cf086fc3a3cffe4c96fc121983ea037b7503c714
# Parent  5bda008f31c0b12267bbaaa97dc7a5666863739b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03

diff -r 5bda008f31c0 -r cf086fc3a3cf hicQuickQC.xml
--- a/hicQuickQC.xml	Mon Jul 01 18:56:16 2024 +0000
+++ b/hicQuickQC.xml	Mon Nov 04 22:54:21 2024 +0000
@@ -19,11 +19,11 @@
             --restrictionCutFile '$restrictionCutFile'
             
             #if $restrictionSequence:
-                --restrictionSequence '$restrictionSequence'
+                --restrictionSequence $restrictionSequence
             #end if
 
             #if $danglingSequence:
-                --danglingSequence '$danglingSequence'
+                --danglingSequence $danglingSequence
             #end if
             --QCfolder ./QCfolder
 
diff -r 5bda008f31c0 -r cf086fc3a3cf macros.xml
--- a/macros.xml	Mon Jul 01 18:56:16 2024 +0000
+++ b/macros.xml	Mon Nov 04 22:54:21 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
     <token name="@TOOL_VERSION@">3.7.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
@@ -48,14 +48,14 @@
     </xml>
 
     <xml name="restrictionCutFile">
-        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
+        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
                 (i.e. the region between one restriction site and the next)." />
     </xml>
 
     <xml name="restrictionSequence">
         <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
             &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
-            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
+            <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
         </param>
     </xml>
     <xml name="danglingSequence">
@@ -67,7 +67,7 @@
                     This information is easily found on the description of the restriction enzyme.
                     The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
                     A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
-            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
+            <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
         </param>
     </xml>