Mercurial > repos > devteam > samtools_bedcov

diff samtools_bedcov.xml @ 6:762f63d4e25d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 12:58:28 +0000
parents 6856f8a01905
children 09652022e285
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--- a/samtools_bedcov.xml	Mon Nov 20 22:14:28 2023 +0000
+++ b/samtools_bedcov.xml	Thu Jun 19 12:58:28 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.4" profile="@PROFILE@">
+<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.5" profile="@PROFILE@">
     <description>calculate read depth for a set of genomic intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -73,21 +73,25 @@
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
-            <param name="countdel" value="-j" />
+            <param name="countdel" value="true" />
             <output name="output" file="samtools_bedcov_out2.tab" />
         </test>
         <!-- 5) Testing argument -g -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
-            <param name="required_flags" value="2,16,64" />
+            <section name="additional_options">
+                <param name="required_flags" value="2,16,64" />
+            </section>
             <output name="output" file="samtools_depth_out5.tab" />
         </test>
         <!-- 6) Testing argument -G -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
-            <param name="skipped_flags" value="2,16,64" />
+            <section name="additional_options">
+                <param name="skipped_flags" value="2,16,64" />
+            </section>
             <output name="output" file="samtools_depth_out6.tab" />
         </test>
         <!-- 7) Testing depth threshold -d -->