--- a/microsatbed.xml	Sun Jul 21 07:18:47 2024 +0000
+++ b/microsatbed.xml	Wed Aug 14 08:49:28 2024 +0000
@@ -3,12 +3,11 @@
     <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="@VERSION_SUFFIX@">1</token>
         <token name="@PYTHON_VERSION@">3.12.3</token>
-        <token name="@UCSC_VERSION@">455</token>
         <macro name="subsetmacro">
-          <param name="subset" type="select" label="Select at least 1 specific motif length to report" help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more" multiple="true">
+          <param name="subset" type="select" label="Select at least 1 specific motif length to report"
+              help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more" multiple="true">
               <option value="--di" selected="true">All dimers (AC,AG,AT,...)</option>
               <option value="--tri">All trimers (ACG,..)</option>
               <option value="--tetra">All tetramers (ACGT,..)</option>
@@ -20,9 +19,9 @@
     </macros>
     <requirements>
         <requirement version="@PYTHON_VERSION@" type="package">python</requirement>
-        <requirement version="@PYFASTX_VERSION@" type="package">pyfastx</requirement>
+        <requirement version="2.1.0" type="package">pyfastx</requirement>
         <requirement version="@TOOL_VERSION@" type="package">pytrf</requirement>
-        <requirement version="@UCSC_VERSION@" type="package">ucsc-bedgraphtobigwig</requirement>
+        <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
     </requirements>
     <required_files>
         <include path="find_str.py"/>
@@ -30,17 +29,17 @@
     <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
     <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}'
+    #if str($reference_genome.genome_type_select) == "history":
+      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.reffa}'
     #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.reffa.fields.path}'
     #end if
   #else:
     python '${__tool_directory__}/find_str.py'
-    #if $reference_genome.genome_type_select == "history":
-        --fasta '${reference_genome.fasta}'
+    #if str($reference_genome.genome_type_select) == "history":
+        --fasta '${reference_genome.reffa}'
     #else:
-        --fasta '${reference_genome.fasta.fields.path}'
+        --fasta '${reference_genome.reffa.fields.path}'
     #end if
     --bed '$bed'
     #if $mode_cond.mode == "SPECIFIC":
@@ -73,12 +72,12 @@
                 <option value="history" selected="True">Use any fasta file from the current history</option>
             </param>
             <when value="indexed">
-                <param name="fasta" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
+                <param name="reffa" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
                     <options from_data_table="all_fasta"/>
                 </param>
             </when>
             <when value="history">
-                <param name="fasta" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
+                <param name="reffa" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
             </when>
         </conditional>
         <conditional name="mode_cond">
@@ -119,7 +118,7 @@
         <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
     </inputs>
     <outputs>
-      <data name="bed" format="bed" label="STR from $fasta.element_identifier">
+      <data name="bed" format="bed" label="STR in ${on_string}">
         <change_format>
             <when input="mode_cond.outformat" value="gff" format="gff"/>
             <when input="mode_cond.outformat" value="csv" format="csv"/>
@@ -133,7 +132,7 @@
         <test expect_num_outputs="1">
             <conditional name="reference_genome">
                 <param name="genome_type_select" value="history"/>
-                <param name="fasta" value="humsamp.fa"/>
+                <param name="reffa" value="humsamp.fa"/>
             </conditional>
             <conditional name="mode_cond">
                 <param name="mode" value="ALL"/>
@@ -157,7 +156,7 @@
         <test expect_num_outputs="1">
             <conditional name="reference_genome">
                 <param name="genome_type_select" value="history"/>
-                <param name="fasta" value="humsamp.fa"/>
+                <param name="reffa" value="humsamp.fa"/>
             </conditional>
             <conditional name="mode_cond">
                 <param name="mode" value="SPECIFIC"/>
@@ -182,7 +181,7 @@
         <test expect_num_outputs="1">
             <conditional name="reference_genome">
                 <param name="genome_type_select" value="history"/>
-                <param name="fasta" value="mouse.fa"/>
+                <param name="reffa" value="mouse.fa"/>
             </conditional>
             <conditional name="mode_cond">
                 <param name="mode" value="NATIVE"/>
@@ -205,8 +204,8 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="reference_genome">
-                <param name="genome_type_select" value="history"/>
-                <param name="fasta" value="humsamp.fa"/>
+                <param name="genome_type_select" value="indexed"/>
+                <param name="reffa" value="hgtest"/>
             </conditional>
             <conditional name="mode_cond">
                 <param name="mode" value="SPECIFICBW"/>