diff microsatbed.xml @ 4:25c70fff4079 draft default tip

planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59

--- a/microsatbed.xml	Sun Jul 14 03:55:47 2024 +0000
+++ b/microsatbed.xml	Sun Jul 14 23:52:21 2024 +0000
@@ -1,4 +1,4 @@
-<tool name="strtobed" id="microsatbedfubar" version="1.3.0" profile="22.05">
+<tool name="STR to bed" id="microsatbed" version="1.3.0" profile="22.05">
   <description>Short Tandem Repeats to bed features from fasta</description>
   <requirements>
     <requirement version="3.12.3" type="package">python</requirement>
@@ -11,10 +11,18 @@
    <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
   <command><![CDATA[
   #if $mode_cond.mode == "NATIVE":
-    pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}' 
+    #if $reference_genome.genome_type_select == "history":
+      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}'
+    #else:
+      pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta.fields.path}'
+    #end if
   #else:
     python '${__tool_directory__}/find_str.py'
-    --fasta '${reference_genome.fasta}' 
+    #if $reference_genome.genome_type_select == "history":
+      --fasta '${reference_genome.fasta}'
+    #else:
+      --fasta '${reference_genome.fasta.fields.path}'
+    #end if
     --bed '$bed'
     #if $mode_cond.mode == "SPECIFIC":
     --specific '$mode_cond.specific'
@@ -51,15 +59,12 @@
     <conditional name="reference_genome">
         <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
             <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
-            <option selected="True" value="history">Use any fasta file from the current history</option>
+            <option value="history" selected="True">Use any fasta file from the current history</option>
         </param>
         <when value="indexed">
-            <param name="fasta" type="select" optional="false" multiple="false" label="Choose a built-in, or custom reference genome" 
-                help="If the genome you need is not on the list, add a custom genome or choose a genome fasta from the current history">
-                <options from_data_table="all_fasta">
-                    <filter column="2" type="sort_by"/>
-                    <validator message="No genomes are available" type="no_options"/>
-                </options>
+            <param name="fasta" type="select" multiple="false" 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">
@@ -98,17 +103,17 @@
     </when>
     <when value="NATIVE">
       <param name="outformat" type="select" optional="false" label="Select the required output format" 
-        help="Pytrf can create GFF, CSV or TSV output files">
-        <option value="gff" selected="true">GFF</option>
+        help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below">
+        <option value="gff" >GFF</option>
         <option value="csv">Comma separated values</option>
-        <option value="tsv">Tab separated values</option>
+        <option value="tsv" selected="true">Tab separated values</option>
       </param>
+      <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
       <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/>
       <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/>
       <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/>
       <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/>
       <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/>
-      <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/>
     </when>
     </conditional>
   </inputs>