# HG changeset patch
# User iuc
# Date 1728133707 0
# Node ID 71ad4a56c40c60a7ac9b6313040a4f59fa0a67fd
# Parent  9570563fb686db706302c2c879214c63418b0ef6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a

diff -r 9570563fb686 -r 71ad4a56c40c macros.xml
--- a/macros.xml	Sat Sep 28 16:40:55 2024 +0000
+++ b/macros.xml	Sat Oct 05 13:08:27 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 9570563fb686 -r 71ad4a56c40c umi-tools_counts.xml
--- a/umi-tools_counts.xml	Sat Sep 28 16:40:55 2024 +0000
+++ b/umi-tools_counts.xml	Sat Oct 05 13:08:27 2024 +0000
@@ -1,9 +1,9 @@
 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>performs quantification of UMIs from BAM files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <!-- TODO see comment in LINK_SAM_BAM_INPUT -->
         <requirement type="package" version="1.12">samtools</requirement>
@@ -33,7 +33,7 @@
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" help="Please use the samtools sort tool to ensure a correct BAM input" />
-        <param argument="--wide-format-cell-counts" name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
+        <param name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
         <expand macro="barcode_options_macro"/>
         <expand macro="umi_grouping_options_macro"/>
         <expand macro="sambam_options_macro"/>
@@ -66,7 +66,7 @@
         <expand macro="log_output_macro"/>
     </outputs>
     <tests>
-        <test><!--count_single_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -85,7 +85,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_gene_tag.tsv" />
         </test>
-        <test><!--count_single_gene_tag .. with sam input-->
+        <test expect_num_outputs="1"><!--count_single_gene_tag .. with sam input-->
             <param name="input" value="chr19_gene_tags.sam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -104,7 +104,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_gene_tag.tsv" />
         </test>
-        <test><!--count_single_cells_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_cells_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -123,7 +123,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
         </test>
-        <test><!--count_single_cells_wide_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_cells_wide_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -142,7 +142,7 @@
             <param name="wide_format_cell_counts" value="true" />
             <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
         </test>
-        <test><!-- count ENSDARG00000019692, with defaults -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, with defaults -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
@@ -156,7 +156,7 @@
             </section>
             <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
         </test>
-        <test><!-- count ENSDARG00000019692, relabel string -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel string -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
@@ -174,7 +174,7 @@
             </conditional>
             <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
         </test>
-        <test><!-- count ENSDARG00000019692, relabel filename -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel filename -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />