# HG changeset patch
# User iuc
# Date 1726316222 0
# Node ID 5f8efb080f49237ebda6694a1ef6dc7e8095a054
# Parent  8c8299e553ec595359fb7b72401a8a97554a9dae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6

diff -r 8c8299e553ec -r 5f8efb080f49 find_str.py
--- a/find_str.py	Thu Sep 12 15:41:01 2024 +0000
+++ b/find_str.py	Sat Sep 14 12:17:02 2024 +0000
@@ -7,6 +7,7 @@
 """
 Allows all STR or those for a subset of motifs to be written to a bed file
 Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
+Note that there are only four possible types of dinucleotide repeat, because CA = AC = GT = TG, GA = AG = CT = TC, AT = TA, and GC = CG.
 """
 
 
@@ -22,7 +23,7 @@
         bin = int(b[1] / winwidth)
         d[bin] += nt
     bedg = [
-        (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x]))
+        (name, (x * winwidth), ((x + 1) * winwidth), float(d[x]))
         for x in range(nwin + 1)
         if (x + 1) * winwidth <= chrlen
     ]
@@ -82,13 +83,13 @@
                 cbed.append(row)
         if args.bigwig:
             w = getDensity(name, cbed, chrlen, args.winwidth)
-            wig += w
-        bed += cbed
+            wig.extend(w)
+        bed.extend(cbed)
     if args.bigwig:
         wig.sort()
-        bedg = ["%s %d %d %.2f" % x for x in wig]
         with open("temp.bedg", "w") as bw:
-            bw.write("\n".join(bedg))
+            for row in wig:
+                bw.write("%s %d %d %.2f\n" % row)
         chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
         with open("temp.chromlen", "w") as cl:
             cl.write("\n".join(chroms))
@@ -96,10 +97,9 @@
         subprocess.run(cmd)
     else:
         bed.sort()
-        obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
         with open(args.bed, "w") as outbed:
-            outbed.write("\n".join(obed))
-            outbed.write("\n")
+            for row in bed:
+                outbed.write("%s\t%d\t%d\t%s_%d\t%d\n" % row)
 
 
 if __name__ == "__main__":
diff -r 8c8299e553ec -r 5f8efb080f49 microsatbed.xml
--- a/microsatbed.xml	Thu Sep 12 15:41:01 2024 +0000
+++ b/microsatbed.xml	Sat Sep 14 12:17:02 2024 +0000
@@ -3,7 +3,7 @@
     <description>Short Tandem Repeats to bed features from fasta</description>
     <macros>
         <token name="@TOOL_VERSION@">1.3.3</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PYTHON_VERSION@">3.12.3</token>
         <macro name="subsetmacro">
           <param name="subset" type="select" label="Select at least 1 specific motif length to report"
@@ -217,9 +217,9 @@
             <param name="tetramin" value="20"/>
             <param name="pentamin" value="20"/>
             <param name="hexamin" value="20"/>
-            <output name="bed" value="dibed_wig_sample" compare="sim_size" delta="10">
+            <output name="bed" value="dibed_indexed_sample" compare="sim_size" delta="10">
               <assert_contents>
-                <has_size value="73544" delta="10" />
+                <has_size value="67559" delta="10" />
               </assert_contents>
             </output>
         </test>
diff -r 8c8299e553ec -r 5f8efb080f49 test-data/dibed_indexed_sample
Binary file test-data/dibed_indexed_sample has changed
diff -r 8c8299e553ec -r 5f8efb080f49 test-data/dibed_wig_sample
Binary file test-data/dibed_wig_sample has changed