# HG changeset patch
# User iuc
# Date 1740775144 0
# Node ID 3b96947e95a8fd0167076768c3cc0476f4e7b949
# Parent  b015f2183a2c10784c7189111767a15144fe1ece
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e

diff -r b015f2183a2c -r 3b96947e95a8 macros.xml
--- a/macros.xml	Wed Jan 29 10:06:52 2025 +0000
+++ b/macros.xml	Fri Feb 28 20:39:04 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 b015f2183a2c -r 3b96947e95a8 test-data/dedup_out1.bam
Binary file test-data/dedup_out1.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 test-data/dedup_out2.bam
Binary file test-data/dedup_out2.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 test-data/dedup_out3.bam
Binary file test-data/dedup_out3.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 test-data/dedup_out4.bam
Binary file test-data/dedup_out4.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 test-data/dedup_out5.bam
Binary file test-data/dedup_out5.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 test-data/dedup_out6.bam
Binary file test-data/dedup_out6.bam has changed
diff -r b015f2183a2c -r 3b96947e95a8 umi-tools_extract.xml
--- a/umi-tools_extract.xml	Wed Jan 29 10:06:52 2025 +0000
+++ b/umi-tools_extract.xml	Fri Feb 28 20:39:04 2025 +0000
@@ -83,7 +83,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_types">
-                <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
+            <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
         </expand>
         <expand macro="fastq_barcode_extraction_options_macro"/>
 
@@ -134,8 +134,8 @@
             <conditional name="extract_method_cond">
                 <param name="prime3" value="true" />
             </conditional>
-            <param name="quality_selector" value="true" />
-            <param name="quality_filter_threshold" value="10" />
+            <param name="quality|quality_selector" value="true" />
+            <param name="quality|quality_filter_threshold" value="10" />
             <param name="log" value="true"/>
             <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
             <output name="out_log" >
@@ -166,7 +166,6 @@
         <test expect_num_outputs="4">
             <conditional name="input_type_cond">
                 <param name="input_type" value="paired_collection" /> <!-- same as before, but uncompressed -->
-                <param name="paired_type" value="no" />
                 <param name="input_readpair">
                     <collection type="paired" >
                         <element name="forward" ftype="fastqsanger" value="t_R1.fastq" />
@@ -194,7 +193,7 @@
                 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
             </conditional>
-            <param name="extract_method" value="string" />
+            <param name="extract_method_cond|extract_method" value="string" />
             <param name="whitelist" value="scrb_seq_barcodes" />
             <param name="log" value="true"/>
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true"  ftype="fastqsanger.gz" />
@@ -206,7 +205,7 @@
                 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
             </conditional>
-            <param name="extract_method" value="regex" />
+            <param name="extract_method_cond|extract_method" value="regex" />
             <param name="whitelist" value="scrb_seq_barcodes" />
             <param name="log" value="true"/>
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
@@ -218,7 +217,7 @@
                 <param name="input_read2" value="read_R2.200.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="NNNNNNCCCCCC" />
             </conditional>
-            <param name="extract_method" value="string" />
+            <param name="extract_method_cond|extract_method" value="string" />
             <output name="out" file="read_R1.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
             <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
         </test>