From 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Tue, 2 Apr 2024 23:40:43 +1100
Subject: [PATCH] Need bai for dexseq-count (#5926)

* update only count

* bump version

* moar quotes!

* try new biocontainer
---
 tools/dexseq/dexseq_count.xml | 22 ++++++++++++----------
 tools/dexseq/macros.xml       |  5 ++---
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/tools/dexseq/dexseq_count.xml b/tools/dexseq/dexseq_count.xml
index 86ead2843c1..32c7c3d3313 100644
--- a/tools/dexseq/dexseq_count.xml
+++ b/tools/dexseq/dexseq_count.xml
@@ -16,18 +16,20 @@
     <command><![CDATA[
 #if $mode.mode_select == "prepare":
     dexseq_prepare_annotation.py
-        -r $mode.aggregate
-        '$mode.gtffile'
+        -r '${mode.aggregate}'
+        '${mode.gtffile}'
         '$flattened_gtf_out'
 #elif $mode.mode_select == "count":
+    ln -s -f '${mode.bamfile}' 'input.bam' &&
+    ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' &&
     dexseq_count.py
         --format bam
-        --paired $mode.paired
-        --stranded $mode.stranded
-        --minaqual $mode.qual
-        --order $mode.order
-        $mode.flattened_gtf_in
-        '$mode.bamfile'
+        --paired '${mode.paired}'
+        --stranded '${mode.stranded}'
+        --minaqual '${mode.qual}'
+        --order '${mode.order}'
+        '${mode.flattened_gtf_in}'
+        'input.bam'
         '$counts_file'
     &&
     sed -i 's/\"//g' '$counts_file'
@@ -73,14 +75,14 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="prepare" />
             <param name="gtffile" ftype="gff" value="original.gtf"/>
             <param name="aggregate" value="True"/>
             <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
         </test>
         <!-- Ensure count mode works -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="count" />
             <param name="bamfile" ftype="bam" value="in.bam" />
             <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
diff --git a/tools/dexseq/macros.xml b/tools/dexseq/macros.xml
index 9221feac819..c5d58dd360a 100644
--- a/tools/dexseq/macros.xml
+++ b/tools/dexseq/macros.xml
@@ -1,12 +1,11 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.44</token>
+    <token name="@TOOL_VERSION@">1.48.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement>
-            <requirement type="package" version="1.20.3">r-getopt</requirement>
+            <requirement type="package" version="1.20.4">r-getopt</requirement>
             <requirement type="package" version="0.2.21">r-rjson</requirement>
         </requirements>
     </xml>