# HG changeset patch
# User iuc
# Date 1753273333 0
# Node ID a3e78550e42e6fcecda01b4f94a4b62176dfa352
# Parent  31d5c8c3addee71dd45161712ce7860f42aa92f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 1471c6728550f057b36d5bb1f54df4a8fb5236a4

diff -r 31d5c8c3adde -r a3e78550e42e gffcompare.xml
--- a/gffcompare.xml	Tue May 13 19:03:48 2025 +0000
+++ b/gffcompare.xml	Wed Jul 23 12:22:13 2025 +0000
@@ -1,5 +1,5 @@
 <tool id="gffcompare" name="GffCompare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
-    <description>compare assembled transcripts to a reference annotation</description>
+    <description>Compare assembled transcripts to a reference annotation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -255,12 +255,12 @@
             </output>
             <output name="transcripts_tracking">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined">
                 <assert_contents>
-                    <has_n_lines n="18"/>
+                    <has_n_lines n="16"/>
                 </assert_contents>
             </output>
             <output_collection name="tmap_output_collection" type="list" count="2"/>
@@ -307,12 +307,12 @@
             </output>
             <output name="transcripts_tracking">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined">
                 <assert_contents>
-                    <has_n_lines n="18"/>
+                    <has_n_lines n="16"/>
                 </assert_contents>
             </output>
         </test>
@@ -358,12 +358,12 @@
             </output>
             <output name="transcripts_tracking">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined">
                 <assert_contents>
-                    <has_n_lines n="18"/>
+                    <has_n_lines n="16"/>
                 </assert_contents>
             </output>
         </test>
@@ -373,7 +373,7 @@
             <conditional name="conditional_annotation">
                 <param name="selector" value="yes"/>
                 <conditional name="ref_source">
-                    <param name="ref_source_sel" value="history"/>
+                    <param name="selector" value="history"/>
                     <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/>
                 </conditional>
                 <conditional name="conditional_strict">
@@ -382,7 +382,7 @@
                 </conditional>
             </conditional>
             <conditional name="seq_data">
-                <param name="seletor" value="no"/>
+                <param name="selector" value="no"/>
             </conditional>
             <assert_command>
                 <not_has_text text="-R "/>
@@ -404,23 +404,23 @@
             </assert_command>
             <output name="transcripts_stats" ftype="txt">
                 <assert_contents>
-                    <has_line line=" Total union super-loci across all input datasets: 7 "/>
+                    <has_line line=" Total union super-loci across all input datasets: 6 "/>
                     <has_line line="#gffcompare -V -r reference_annotation --strict-match -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/>
                 </assert_contents>
             </output>
             <output name="transcripts_loci" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="7"/>
+                    <has_n_lines n="6"/>
                 </assert_contents>
             </output>
             <output name="transcripts_tracking" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined" ftype="gtf">
                 <assert_contents>
-                    <has_n_lines n="18"/>
+                    <has_n_lines n="16"/>
                 </assert_contents>
             </output>
             <output_collection name="refmap_output_collection" type="list" count="2"/>
@@ -432,7 +432,7 @@
             <conditional name="conditional_annotation">
                 <param name="selector" value="yes"/>
                 <conditional name="ref_source">
-                    <param name="ref_source_sel" value="cached"/>
+                    <param name="selector" value="cached"/>
                     <param name="index" value="test_buildid"/>
                 </conditional>
                 <param name="R" value="true"/>
@@ -489,16 +489,16 @@
                     <has_n_lines n="0"/>
                 </assert_contents>
             </output>
-            <output_collection name="refmap_output_collection" type="list" count="0"/> <!-- because of -M no refmaps are created -->
+            <output_collection name="refmap_output_collection" type="list" count="2"/>
             <output_collection name="tmap_output_collection" type="list" count="2"/>
         </test>
-        <!-- Test 06: 2 inputs and reference, non default advanced options -->
+         <!-- Test 06: 2 inputs and reference, non default advanced options -->
         <test expect_num_outputs="6">
             <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/>
             <conditional name="conditional_annotation">
                 <param name="selector" value="yes"/>
                 <conditional name="ref_source">
-                    <param name="ref_source_sel" value="history"/>
+                    <param name="selector" value="history"/>
                     <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/>
                 </conditional>
             </conditional>
@@ -532,18 +532,18 @@
             </assert_command>
             <output name="transcripts_stats" ftype="txt">
                 <assert_contents>
-                    <has_line line=" Total union super-loci across all input datasets: 7 "/>
+                    <has_line line=" Total union super-loci across all input datasets: 6 "/>
                     <has_line line="#gffcompare -V -r reference_annotation -d 100 -p OTHER -A -C -X -K gffcompare_in1_gtf gffcompare_in2_gtf"/>
                 </assert_contents>
             </output>
             <output name="transcripts_loci" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="7"/>
+                    <has_n_lines n="6"/>
                 </assert_contents>
             </output>
             <output name="transcripts_tracking" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined" ftype="gtf">
@@ -561,7 +561,7 @@
             <conditional name="conditional_annotation">
                 <param name="selector" value="yes"/>
                 <conditional name="ref_source">
-                    <param name="ref_source_sel" value="history"/>
+                    <param name="selector" value="history"/>
                     <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/>
                 </conditional>
             </conditional>
@@ -587,23 +587,23 @@
             </assert_command>
             <output name="transcripts_stats" ftype="txt">
                 <assert_contents>
-                    <has_line line=" Total union super-loci across all input datasets: 7 "/>
+                    <has_line line=" Total union super-loci across all input datasets: 6 "/>
                     <has_line line="#gffcompare -V -r reference_annotation -T -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/>
                 </assert_contents>
             </output>
             <output name="transcripts_loci" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="7"/>
+                    <has_n_lines n="6"/>
                 </assert_contents>
             </output>
             <output name="transcripts_tracking" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="9"/>
+                    <has_n_lines n="8"/>
                 </assert_contents>
             </output>
             <output name="transcripts_combined" ftype="gtf">
                 <assert_contents>
-                    <has_n_lines n="18"/>
+                    <has_n_lines n="16"/>
                 </assert_contents>
             </output>
         </test>
@@ -614,7 +614,7 @@
             <conditional name="conditional_annotation">
                 <param name="selector" value="yes"/>
                 <conditional name="ref_source">
-                    <param name="ref_source_sel" value="history"/>
+                    <param name="selector" value="history"/>
                     <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf"/>
                 </conditional>
                 <param name="R" value="true"/>
@@ -628,13 +628,13 @@
             <param name="max_dist_group" value="100"/>
             <output name="transcripts_stats" ftype="txt">
                 <assert_contents>
-                    <has_line line=" Total union super-loci across all input datasets: 29 "/>
+                    <has_line line=" Total union super-loci across all input datasets: 21 "/>
                     <has_line line="#gffcompare -V -r reference_annotation -R --strict-match -e 100 -T -d 100 -p TCONS gffcompare_in4_gtf"/>
                 </assert_contents>
             </output>
             <output name="transcripts_loci" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="29"/>
+                    <has_n_lines n="21"/>
                 </assert_contents>
             </output>
             <output name="transcripts_tracking" ftype="tabular">
diff -r 31d5c8c3adde -r a3e78550e42e macros.xml
--- a/macros.xml	Tue May 13 19:03:48 2025 +0000
+++ b/macros.xml	Wed Jul 23 12:22:13 2025 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.12.9</token>
+    <token name="@TOOL_VERSION@">0.12.10</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">gffcompare</requirement>
-            <requirement type="package" version="1.21">samtools</requirement>
+            <requirement type="package" version="1.22.1">samtools</requirement>
         </requirements>
     </xml>
     <xml name="citations">