diff hicFindRestrictionSites.xml @ 9:6c5097f6d41e draft

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

--- a/hicFindRestrictionSites.xml	Tue Jan 10 19:12:06 2023 +0000
+++ b/hicFindRestrictionSites.xml	Wed Oct 18 10:10:03 2023 +0000
@@ -8,17 +8,20 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
             --fasta '$fasta'
-            --searchPattern '$searchPattern'
+            #set $searchPatternList = ' '.join([ '\'%s\'' % $pattern for $pattern in str($searchPattern).split(' ') ])
+
+            --searchPattern '$searchPatternList'
             --outFile restriction_site.bed
 
     ]]>    </command>
     <inputs>
-        <param argument="--fasta" type="data" format='fasta,fasta.gz' label="Fasta file for the organism genome." help="The organism genome fasta file to compute the restriction enzyme position." />
+        <param argument="--fasta" type="data" format="fasta,fasta.gz" label="Fasta file for the organism genome." 
+            help="The organism genome fasta file to compute the restriction enzyme position." />
         <param argument="--searchPattern" type="text" value="" label="Restriction enzyme sequence" help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\".
-                    Both, forward and reverse strand are searched for a match. The pattern
-                    is a regexp and can contain regexp specif syntax
-                    (see https://docs.python.org/2/library/re.html). For example the pattern
-                    CG..GC will find all occurrence of CG followed by any two bases and then GC.'>
+            Both, forward and reverse strand are searched for a match. The pattern
+            is a regexp and can contain regexp specif syntax
+            (see https://docs.python.org/2/library/re.html). For example the pattern
+            CG..GC will find all occurrence of CG followed by any two bases and then GC.'>
             <validator type="expression" message="Only ASCII characters are allowed."><![CDATA[all(ord(c) < 128 for c in value)]]></validator>
         </param>
     </inputs>