Mercurial > repos > iuc > samtools_ampliconclip

diff samtools_ampliconclip.xml @ 4:f597cb9b33bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 12:58:20 +0000
parents 6a8febad1f6c
children f20b704ba069
line wrap: on
line diff
--- 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>