# HG changeset patch
# User iuc
# Date 1728133684 0
# Node ID c5a2ee07c4e14f6bd8fcf350ec806c3588e27412
# Parent  04e09969d376b8e069bf2f43f56802be2d7feabc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a

diff -r 04e09969d376 -r c5a2ee07c4e1 macros.xml
--- a/macros.xml	Sat Sep 28 16:40:30 2024 +0000
+++ b/macros.xml	Sat Oct 05 13:08:04 2024 +0000
@@ -4,8 +4,8 @@
     <!-- macros applying to all umi_tools -->
 
     <token name="@TOOL_VERSION@">1.1.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">21.01</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">23.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
@@ -104,8 +104,8 @@
                 <expand macro="barcode1_macro"/>
             </when>
             <when value="paired">
-                <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
-                <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
+                <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Forward reads in FASTQ format" />
+                <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reverse reads in FASTQ format" />
                 <expand macro="barcode1_macro"/>
                 <expand macro="barcode2_macro"/>
                 <yield/>
@@ -152,11 +152,11 @@
 
     <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
         #if $input.is_of_type("sam"):
-            ## TODO dedup has problems with SAM input in some cases
+            ## sam input is not supported for paired data
             ## https://github.com/CGATOxford/UMI-tools/issues/483
-            ## so convert it to sorted BAM for now
+            ## so convert it to sorted BAM
             ## #set $input_file = $input
-            samtools sort --no-PG '$input' > 'input.bam' &&
+            samtools sort --no-PG '$input' -O BAM > 'input.bam' &&
             samtools index -b 'input.bam' &&
             #set $input_file = 'input.bam'
         #else:
@@ -166,7 +166,7 @@
         #end if
     ]]></token>
     <token name="@SET_INPUT_TYPE@"><![CDATA[
-        ## TODO see comment in LINK_SAM_BAM_INPUT
+        ## see comment in LINK_SAM_BAM_INPUT
         ## #if $input.is_of_type("sam"):
         ##     --in-sam
         ## #end if
@@ -511,12 +511,12 @@
             <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
                 <expand macro="sanitize_tag" />
             </param>
-            <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
+            <param argument="--skip-tags-regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
                 <expand macro="barcode_sanitizer" />
             </param>
             <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
             <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
-            <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
+            <param argument="--per-cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
         </section>
     </xml>
     <token name="@SC_OPTIONS@"><![CDATA[
diff -r 04e09969d376 -r c5a2ee07c4e1 umi-tools_dedup.xml
--- a/umi-tools_dedup.xml	Sat Sep 28 16:40:30 2024 +0000
+++ b/umi-tools_dedup.xml	Sat Oct 05 13:08:04 2024 +0000
@@ -1,9 +1,9 @@
 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Extract UMI from fastq files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <requirement type="package" version="1.21">samtools</requirement>
     </expand>
@@ -22,7 +22,7 @@
             @FULLSC_OPTIONS@
             @ADVANCED_OPTIONS@
             -I '$input_file' -S deduped.bam
-            ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy
+            ## using samtools sort is a workaround, for the following error that appears when Galaxy
             ## compares the generated file with the one in test-data
             ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
             ## problem seems to be the BAM file generated with pysam