--- a/tRNAscan.xml	Wed Jul 26 10:14:05 2017 -0400
+++ b/tRNAscan.xml	Tue Oct 28 09:15:42 2025 +0000
@@ -1,74 +1,112 @@
-<tool id="trnascan" name="tRNA prediction" version="0.4">
-    <description>(tRNAscan)</description>
+<tool id="trnascan" name="tRNA prediction" version="@TOOL_VERSION@" profile="24.0">
+    <description>using tRNAscan, EufindtRNA &amp; tRNA covariance models</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.12</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">trnascan-se</xref>
+    </xrefs>
     <requirements>
-      <requirement type="package" version="1.3.1">trnascan-se</requirement>
-      <requirement type="package" version="1.0.2">infernal</requirement>
-      <requirement type="package" version="1.70">biopython</requirement>
-      <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">trnascan-se</requirement>
     </requirements>
     <command>
-      <![CDATA[
-python '$__tool_directory__/tRNAscan.py'
-#if $organism
-    $organism
-#end if
+        <![CDATA[
+tRNAscan-SE --forceow --hitsrc --quiet --brief
+$organism
 #if $mode
     $mode
 #end if
-#if $showPrimSecondOpt
-    $showPrimSecondOpt
+$breakdown
+$nopseudo
+$codons
+#if $missed
+--missed '$fasta_missed'
 #end if
-#if $disablePseudo
-    $disablePseudo
-#end if
-#if $showCodons
-    $showCodons
+#if $stats
+--stats '$stats_txt'
 #end if
 -o
 '$tabular_output'
+--fasta '$fasta_output'
+--thread \${GALAXY_SLOTS:-4}
 '$inputfile'
-'$fasta_output'
       ]]>
     </command>
     <inputs>
         <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
-        <param name="organism" type="select" label="Select Organism">
-            <option value="" selected="true">Eukaryotic</option>
-            <option value="-G">general tRNA model</option>
+        <param name="organism" type="select" label="Select Organism/Domain">
+            <option value="-E" selected="true">Eukaryotic</option>
             <option value="-B">Bacterial</option>
             <option value="-A">Archaeal</option>
-            <option value="-O">Mitochondrial/Chloroplast</option>
+            <option value="-G">General tRNA model (incl. Eukaryotic, Bacterial and Archaeal cytoslic tRNAs)</option>
+            <option value="-M mammal">Mammalian Mitochondrial tRNAs</option>
+            <option value="-M vert">Vertebrate Mitochondrial tRNAs</option>
+            <option value="-O">Other organellar tRNAs</option>
         </param>
         <param name="mode" type="select" label="Select Mode">
             <option value="" selected="true">Default</option>
-            <option value="-C">Covariance model analysis only (slow)</option>
-            <option value="-T">tRNAscan only</option>
-            <option value="-E">EufindtRNA only</option>
-            <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option> 
-            <option value="--newscan">Infernal and new cm models</option>
+            <option value="-I">Search using Infernal</option>
+            <option value="--max">Search using Infernal without hmm filter (very slow)</option>
+            <option value="-L">Search using the legacy method (tRNAscan, EufindtRNA, and COVE)</option>
+            <option value="--cove">Covariance model analysis only (legacy, extremely slow)</option>
+            <option value="--tscan">tRNAscan only</option>
+            <option value="--eufind">EufindtRNA only</option>
         </param>
-        <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" />
-        <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" />
-        <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" />
+        <param argument="--nopseudo" type="boolean" label="Disable pseudogene checking" truevalue="--nopseudo" falsevalue="" checked="False"/>
+        <param argument="--breakdown" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="--breakdown" falsevalue="" checked="False"/>
+        <param argument="--codons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="--codons" falsevalue="" />
+        <param argument="--missed" type="boolean" label="Save all seqs that do NOT have at least one tRNA prediction in them" checked="False"/>
+        <param argument="--stats" type="boolean" label="Save statistics (speed, # tRNAs found in each part of search, etc)" checked="False"/>
     </inputs>
     <outputs>
         <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" />
-        <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" />
+        <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: predicted fasta" />
+        <data format="fasta" name="fasta_missed" label="${tool.name} on ${on_string}: missed fasta">
+            <filter>missed is True</filter>
+        </data>
+        <data format="txt" name="stats_txt" label="${tool.name} on ${on_string}: stats">
+            <filter>stats is True</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="inputfile" value="trna_arabidopsis.fasta" ftype="fasta" />
-            <param name="organism" value="" />
-            <param name="mode" value="--infernal" /> <!-- Infernal test not working due to cmsearch error-->
-            <param name="disablePseudo" value="" />
-            <param name="showPrimSecondOpt" value="" />
-            <param name="showCodons" value="" />
-            <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.fasta" ftype="fasta" />
-            <output name="tabular_output" file="tRNAscan_eukaryotic_infernal.tabular" ftype="tabular" />
+            <param name="organism" value="-E" />
+            <param name="mode" value="-I" />
+            <param name="breakdown" value="True" />
+            <param name="codons" value="True" />
+            <param name="missed" value="True" />
+            <param name="stats" value="True" />
+            <output name="tabular_output" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="gi|240255695:23036500-23037000 \t1\t381\t453\tAla\tGCA\t0\t0\t66.6\tInf\t"/>
+                </assert_contents>
+            </output>
+            <output name="fasta_output" ftype="fasta">
+                <assert_contents>
+                    <has_line line=">gi|240255695:23036500-23037000.trna1 gi|240255695:23036500-23037000:381-453 (+) Ala (TGC) 73 bp Sc: 66.6"/>
+                    <has_line line="GGGGATGTAGCTCATATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACAGGGTTCGATT"/>
+                </assert_contents>
+            </output>
+            <output name="fasta_missed" ftype="fasta">
+                <assert_contents>
+                    <has_text text=">dummy_seq"/>
+                    <has_text text="ACTGACTGATCGTAACTAGTAGCGACTGATCGATCGTACTGCATGGCATGTGACTGTCCG"/>
+                </assert_contents>
+            </output>
+            <output name="stats_txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="Bases read:             571"/>
+                    <has_line line="Bases in tRNAs:         73"/>
+                    <has_line line="tRNAs predicted:        1"/>
+                    <has_line line="Infernal-confirmed tRNAs:     1"/>
+                    <has_line_matching expression="Ala     : 1\t  AGC:         GGC:         CGC:         TGC:       "/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
-<![CDATA[
+        <![CDATA[
 
 
 **What it does**
@@ -79,7 +117,7 @@
 eubacterial sequences, but it may be applied more broadly with a
 slight reduction in sensitivity.
 
-.. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
+.. _tRNAscan-SE: https://github.com/UCSC-LoweLab/tRNAscan-SE
 
 **Input**
 
@@ -232,6 +270,6 @@
 ]]>
     </help>
     <citations>
-        <citation type="doi">10.1093/nar/25.5.0955</citation>
+        <citation type="doi">10.1093/nar/gkab688</citation>
     </citations>
 </tool>