Teloscope v0.1.3 (#7508)

* Update to Teloscope v0.1.3

* Update Teloscope wrapper for v0.1.3

* Add tests for --edit-distance parameter

Author: AldhairMedico

tools/teloscope/macros.xml

@@ -4,7 +4,7 @@
             <requirement type="package" version="@TOOL_VERSION@">teloscope</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.1.2</token>
+    <token name="@TOOL_VERSION@">0.1.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.02</token>
     <xml name="citations">

tools/teloscope/teloscope.xml

@@ -20,6 +20,7 @@
             --max-block-distance '$max_block_distance'
             --min-block-length '$min_block_length'
             --min-block-density '$min_block_density'
+            --edit-distance '$edit_distance'
             
             $out_win_repeats
             $out_gc
@@ -57,6 +58,7 @@
         <param argument="--max-block-distance" type="integer" min="0" value="200" label="Maximum block distance for merging"/>
         <param argument="--min-block-length" type="integer" min="0" value="500" label="Minimum block length"/>
         <param argument="--min-block-density" type="float" min="0" max="1" value="0.5" label="Minimum block density (0–1)"/>
+        <param argument="--edit-distance" type="integer" min="0" max="2" value="0" label="Edit distance for pattern matching (0–2)"/>
 
         <param argument="--out-win-repeats" type="boolean" truevalue="--out-win-repeats" falsevalue="" checked="false" label="Window repeat counts"/>
         <param argument="--out-gc" type="boolean" truevalue="--out-gc" falsevalue="" checked="false" label="Window GC"/>
@@ -161,6 +163,48 @@
                 </assert_contents>
             </output>
         </test>
+
+        <!-- 3) Edit distance 1: more variants detected -->
+        <test expect_num_outputs="2">
+            <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
+            <param name="canonical" value="TTAGGG"/>
+            <param name="patterns" value="TTAGGG,CCCTAA"/>
+            <param name="edit_distance" value="1"/>
+            <output name="terminal_telomeres">
+                <assert_contents>
+                    <!-- p-arm telomere with extended start due to edit distance -->
+                    <has_text text="chr33_mat&#9;442&#9;14354&#9;13912&#9;p&#9;"/>
+                    <!-- q-arm telomere -->
+                    <has_text text="chr33_mat&#9;4219967&#9;4246337&#9;26370&#9;q&#9;"/>
+                </assert_contents>
+            </output>
+            <output name="telo_report">
+                <assert_contents>
+                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- 4) Edit distance 2: maximum variants detected -->
+        <test expect_num_outputs="2">
+            <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
+            <param name="canonical" value="TTAGGG"/>
+            <param name="patterns" value="TTAGGG,CCCTAA"/>
+            <param name="edit_distance" value="2"/>
+            <output name="terminal_telomeres">
+                <assert_contents>
+                    <!-- p-arm telomere extends to position 1 with edit distance 2 -->
+                    <has_text text="chr33_mat&#9;1&#9;14354&#9;14353&#9;p&#9;"/>
+                    <!-- q-arm telomere -->
+                    <has_text text="chr33_mat&#9;4219967&#9;4246337&#9;26370&#9;q&#9;"/>
+                </assert_contents>
+            </output>
+            <output name="telo_report">
+                <assert_contents>
+                    <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -187,8 +231,9 @@
         Key parameters:
         - -c / --canonical: Canonical repeat (default TTAGGG). This is the vertebrate telomeric motif found at chromosome ends that binds to shelterin complex to form a telomere.
         - -p / --patterns: Variant patterns (comma-separated). These are additional telomeric repeat motifs to search for, besides the canonical repeat, it includes other variants that can be part of telomeres.
-        - -w / -s: window size / step (defaults 1000/500)
+        - -w / -s: window size / step (defaults 1000/500).
         - -u / --ultra-fast: terminal scan only (default true); disabled automatically when -g/-e/-r/-m/-i are used.
+        - -x / --edit-distance: Edit Hamming distance for pattern matching (0–2). Useful for identifying degenerate telomeric repeats (default 0).
     ]]></help>
 
     <expand macro="citations"/>