Merge pull request #6519 from bernt-matthias/topic/6505

hicexplorer: fix restriction/danglingSequence
galaxyproject · Nov 4, 2024 · 79133bc · 79133bc
2 parents a843752 + c02dfbb
commit 79133bc
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/tools/hicexplorer/hicBuildMatrix.xml b/tools/hicexplorer/hicBuildMatrix.xml
@@ -20,10 +20,10 @@
             --restrictionCutFile '$restrictionCutFile'
 
             #if $restrictionSequence:
-                --restrictionSequence '$restrictionSequence'
+                --restrictionSequence $restrictionSequence
             #end if
             #if $danglingSequence:
-                --danglingSequence '$danglingSequence'
+                --danglingSequence $danglingSequence
             #end if
             #if $minDistance:
             --minDistance $minDistance

diff --git a/tools/hicexplorer/hicQuickQC.xml b/tools/hicexplorer/hicQuickQC.xml
@@ -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 --git a/tools/hicexplorer/macros.xml b/tools/hicexplorer/macros.xml
@@ -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>