Mercurial > repos > iuc > umi_tools_dedup

changeset 18:6ec3233f30a6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:41:43 +0000
parents 9cd1c2f5d90e
children
files macros.xml test-data/dedup_out1.bam test-data/dedup_out2.bam test-data/dedup_out3.bam test-data/dedup_out4.bam test-data/dedup_out5.bam test-data/dedup_out6.bam umi-tools_dedup.xml
diffstat 8 files changed, 12 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Jan 29 10:09:34 2025 +0000
+++ b/macros.xml	Fri Feb 28 20:41:43 2025 +0000
@@ -9,7 +9,8 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
-            <yield />
+            <requirement type="package" version="1.21">samtools</requirement>
+            <requirement type="package" version="4.7">sed</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -551,7 +552,9 @@
     <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[
         $gd.buffer_whole_contig
         $gd.whole_contig
-        $gd.multimapping_detection_method
+        #if $gd.multimapping_detection_method
+            --multimapping-detection-method $gd.multimapping_detection_method
+        #end if
     ]]></token>
     
     <xml name="log_input_macro">
Binary file test-data/dedup_out1.bam has changed
Binary file test-data/dedup_out2.bam has changed
Binary file test-data/dedup_out3.bam has changed
Binary file test-data/dedup_out4.bam has changed
Binary file test-data/dedup_out5.bam has changed
Binary file test-data/dedup_out6.bam has changed
--- a/umi-tools_dedup.xml	Wed Jan 29 10:09:34 2025 +0000
+++ b/umi-tools_dedup.xml	Fri Feb 28 20:41:43 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">