changeset 30:53c4f91c6031 draft default tip

planemo upload for repository https://github.com/fubar2/microsatbed commit 80a8c0db54b6e2cab9dfe7178b1e5b3b39592f2c

--- a/find_str.py	Fri Jul 19 23:32:59 2024 +0000
+++ b/find_str.py	Sat Jul 20 01:44:09 2024 +0000
@@ -88,13 +88,13 @@
         bed += cbed
     if args.bigwig:
         wig.sort()
-        bedg = ['%s %d %d %.3f' % x for x in wig]
+        bedg = ["%s %d %d %.3f" % x for x in wig]
         with open("temp.bedg", "w") as bw:
-            bw.write('\n'.join(bedg))
+            bw.write("\n".join(bedg))
         chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
         with open("temp.chromlen", "w") as cl:
-            cl.write('\n'.join(chroms))
-        cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw" ]
+            cl.write("\n".join(chroms))
+        cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw"]
         subprocess.run(cmd)
         shutil.move("temp.bw", args.bed)
     else:

--- a/microsatbed.xml	Fri Jul 19 23:32:59 2024 +0000
+++ b/microsatbed.xml	Sat Jul 20 01:44:09 2024 +0000
@@ -1,10 +1,17 @@
-<tool name="STR to bed" id="microsatbed" version="1.3.2" profile="22.05">
+<tool name="STR to bed" id="microsatbed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
   <description>Short Tandem Repeats to bed features from fasta</description>
+  <macros>
+  <token name="@TOOL_VERSION@">1.3.2</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PYFASTX_VERSION@">2.1.0</token>
+  <token name="@PYTHON_VERSION@">3.12.3</token>
+  <token name="@UCSC_VERSION@">455</token>
+  </macros>
   <requirements>
-    <requirement version="3.12.3" type="package">python</requirement>
-    <requirement version="2.1.0" type="package">pyfastx</requirement>
-    <requirement version="1.3.2" type="package">pytrf</requirement>
-    <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
+    <requirement version="@PYTHON_VERSION@" type="package">python</requirement>
+    <requirement version="@PYFASTX_VERSION@" type="package">pyfastx</requirement>
+    <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement>
+    <requirement version="@UCSC_VERSION@" type="package">ucsc-bedgraphtobigwig</requirement>
      
   </requirements>
    <required_files>
@@ -14,9 +21,9 @@
   <command><![CDATA[
   #if $mode_cond.mode == "NATIVE":
     #if $reference_genome.genome_type_select == "history":
-      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta}'
+      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta}'
     #else:
-      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta.fields.path}'
+      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta.fields.path}'
     #end if
   #else:
     python '${__tool_directory__}/find_str.py'
@@ -129,12 +136,12 @@
       </param>
     </when>
     </conditional>
-    <param type="integer" min="2" name="monomin" value="10"/>
-    <param type="integer" min="1" name="dimin" value="3"/>
-    <param type="integer" min="2" name="trimin" value="2"/>
-    <param type="integer" min="2" name="tetramin" value="2"/>
-    <param type="integer" min="2" name="pentamin" value="2"/>
-    <param type="integer" min="2" name="hexamin" value="2"/>
+    <param type="integer" label="Minimum repeats required for monomers" min="2" name="monomin" value="10"/>
+    <param type="integer" label="Minimum repeats required for dimers" min="1" name="dimin" value="3"/>
+    <param type="integer" label="Minimum repeats required for trimers" min="2" name="trimin" value="2"/>
+    <param type="integer" label="Minimum repeats required for tetramers" min="2" name="tetramin" value="2"/>
+    <param type="integer" label="Minimum repeats required for pentamers" min="2" name="pentamin" value="2"/>
+    <param type="integer" label="Minimum repeats required for hexamers" min="2" name="hexamin" value="2"/>
   </inputs>
   <outputs>
     <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false">