# HG changeset patch
# User iuc
# Date 1740775353 0
# Node ID f19dee633d4a8bb4e7f5696795a74a2c0c00cd17
# Parent  382326c1b1e1cd5953c330502bdc56c0a5b61d7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e

diff -r 382326c1b1e1 -r f19dee633d4a macros.xml
--- a/macros.xml	Wed Jan 29 10:08:15 2025 +0000
+++ b/macros.xml	Fri Feb 28 20:42:33 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">
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out1.bam
Binary file test-data/dedup_out1.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out2.bam
Binary file test-data/dedup_out2.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out3.bam
Binary file test-data/dedup_out3.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out4.bam
Binary file test-data/dedup_out4.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out5.bam
Binary file test-data/dedup_out5.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out6.bam
Binary file test-data/dedup_out6.bam has changed
diff -r 382326c1b1e1 -r f19dee633d4a umi-tools_whitelist.xml
--- a/umi-tools_whitelist.xml	Wed Jan 29 10:08:15 2025 +0000
+++ b/umi-tools_whitelist.xml	Fri Feb 28 20:42:33 2025 +0000
@@ -141,10 +141,10 @@
             <conditional name="extract_method_cond">
                 <param name="prime3" value="false" />
             </conditional>
-            <param name="use_cell_opts" value="advanced" />
+            <param name="celloptions|use_cell_opts" value="advanced" />
+            <param name="celloptions|expect_cells" value="5" />
+            <param name="celloptions|error_correct_threshold" value="3" />
             <param name="knee_method" value="density"/>
-            <param name="expect_cells" value="5" />
-            <param name="error_correct_threshold" value="3" />
             <param name="log" value="true" />
             <output name="out_whitelist" file="out_wl_paired.txt" />
             <output name="out_log" file="out_wl_paired.log" lines_diff="50" />
@@ -167,12 +167,11 @@
             <conditional name="extract_method_cond">
                 <param name="prime3" value="false" />
             </conditional>
-            <param name="use_cell_opts" value="advanced" />
             <param name="knee_method" value="density"/>
-            <param name="expect_cells" value="5" />
-            <param name="error_correct_threshold" value="3" />
+            <param name="celloptions|use_cell_opts" value="advanced" />
+            <param name="celloptions|expect_cells" value="5" />
+            <param name="celloptions|error_correct_threshold" value="3" />
             <param name="log" value="true" />
-            <param name="filtered_out_bool" value="true"/>
             <output name="out_whitelist" file="out_wl_paired.txt" />
             <output name="out_log" file="out_wl_paired.log" lines_diff="50" />
             <output name="out_html_report" file="out_wl_paired.html" />
@@ -183,13 +182,13 @@
             <conditional name="input_type_cond" >
                 <param name="input_type" value="single" />
                 <param name="input_read1" value="testYYY.40k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="bc_pattern" value="(?P&#60;cell_1&#62;.{8,10})(?P&#60;discard_1&#62;ACTGGCCTGCGA){s&#60;=3}(?P&#60;cell_2&#62;.{9})(?P&#60;discard_2&#62;GGTAGCGGTGACA){s&#60;=3}(?P&#60;cell_3&#62;.{9})(?P&#60;umi_1&#62;.{8})T{3}.*" />
             </conditional>
-            <param name="bc_pattern" value="(?P&#60;cell_1&#62;.{8,10})(?P&#60;discard_1&#62;ACTGGCCTGCGA){s&#60;=3}(?P&#60;cell_2&#62;.{9})(?P&#60;discard_2&#62;GGTAGCGGTGACA){s&#60;=3}(?P&#60;cell_3&#62;.{9})(?P&#60;umi_1&#62;.{8})T{3}.*" />
-            <param name="extract_method" value="regex" />
+            <param name="extract_method_cond|extract_method" value="regex" />
+            <param name="extract_method_cond|filtered_out_bool" value="true"/>
             <param name="method" value="umis" />
             <param name="knee_method" value="density"/>
-            <param name="prime3" value="true" />
-            <param name="filtered_out_bool" value="true"/>
+
             <output name="out_whitelist" file="out_wl_user.single.txt" />
             <output name="out_thresh" file="out_wl_user.single.tresh.tab" />
             <output name="out_html_report" file="out_wl_user.single.html" />