# HG changeset patch
# User iuc
# Date 1750337900 0
# Node ID f597cb9b33bf95da7d505013d202d7d73b08246a
# Parent  4967154b98596c9498e51697d7fbc036497b7318
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 4967154b9859 -r f597cb9b33bf macros.xml
--- a/macros.xml	Sun Sep 08 03:25:18 2024 +0000
+++ b/macros.xml	Thu Jun 19 12:58:20 2025 +0000
@@ -11,8 +11,8 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.20</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">1.21</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
@@ -220,6 +220,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r 4967154b9859 -r f597cb9b33bf samtools_ampliconclip.xml
--- a/samtools_ampliconclip.xml	Sun Sep 08 03:25:18 2024 +0000
+++ b/samtools_ampliconclip.xml	Thu Jun 19 12:58:20 2025 +0000
@@ -50,14 +50,14 @@
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bam" value="eboVir3.bam" ftype="bam" />
-            <param name="strand" value="--strand" />
+            <param name="strand" value="true" />
             <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
         </test>
         <!-- 3) testing hard clip-->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bam" value="eboVir3.bam" ftype="bam" />
-            <param name="hard_clip_mode" value="--hard-clip" />
+            <param name="hard_clip_mode" value="true" />
             <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
         </test>
         <!-- 4) testing strand and min length-->
@@ -65,10 +65,10 @@
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bam" value="eboVir3.bam" ftype="bam" />
             <param name="min_length" value="30" />
-            <param name="strand" value="--strand" />
+            <param name="strand" value="true" />
             <param name="tolerance" value="6" />
-            <param name="both_ends" value="--both-ends" />
-            <param name="no_excluded" value="--no-excluded" />
+            <param name="both_ends" value="true" />
+            <param name="no_excluded" value="true" />
             <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
         </test>
         
diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.bam
Binary file test-data/eboVir3.clipped.bam has changed
diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand.bam
Binary file test-data/eboVir3.clipped.strand.bam has changed
diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand_gt30.bam
Binary file test-data/eboVir3.clipped.strand_gt30.bam has changed
diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.clipped.strand_gt30.counts.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.clipped.strand_gt30.counts.tsv	Thu Jun 19 12:58:20 2025 +0000
@@ -0,0 +1,4 @@
+#CHR	LEFT	RIGHT	NAME	SCORE	STRAND	NUM_CLIPPED
+eboVir3	500	1500	1	0	-	113
+eboVir3	1500	2000	2	0	+	42
+eboVir3	1500	3000	3	0	-	141
diff -r 4967154b9859 -r f597cb9b33bf test-data/eboVir3.hardclipped.bam
Binary file test-data/eboVir3.hardclipped.bam has changed