Mercurial > repos > iuc > umi_tools_dedup

diff umi-tools_dedup.xml @ 18:362719583a9f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:39:27 +0000
parents b63f68b03f4a
children
line wrap: on
line diff
--- a/umi-tools_dedup.xml	Wed Jan 29 10:07:15 2025 +0000
+++ b/umi-tools_dedup.xml	Fri Feb 28 20:39:27 2025 +0000
@@ -4,9 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements">
-        <requirement type="package" version="1.21">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @LINK_SAM_BAM_INPUT@
 
@@ -111,12 +109,12 @@
             <output name="output" file="dedup_out4.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="group_in5.bam" ftype="bam" />
+            <param name="input" value="group_in4.bam" ftype="bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
             </section>
             <conditional name="bc">
-                <param name="extract_umi_method" value="read_id" />
+                <param name="extract_umi_method" value="tag" />
                 <param name="umi_tag" value="BX" />
             </conditional>
             <section name="umi">
@@ -125,12 +123,12 @@
             <output name="output" file="dedup_out5.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="group_in6.bam" ftype="bam" />
+            <param name="input" value="group_in4.bam" ftype="bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
             </section>
             <conditional name="bc">
-                <param name="extract_umi_method" value="read_id" />
+                <param name="extract_umi_method" value="tag" />
                 <param name="umi_tag" value="BX" />
             </conditional>
             <section name="umi">
@@ -139,12 +137,12 @@
             <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test expect_num_outputs="5">
-            <param name="input" value="group_in6.bam" ftype="bam" />
+            <param name="input" value="group_in4.bam" ftype="bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
             </section>
             <conditional name="bc">
-                <param name="extract_umi_method" value="read_id" />
+                <param name="extract_umi_method" value="tag" />
                 <param name="umi_tag" value="BX" />
             </conditional>
             <section name="umi">