From 8b4620d84d179c7621321bfa0a9c2e80eea3ef72 Mon Sep 17 00:00:00 2001
From: Gautam Naishadham <gnaishadham@neb.com>
Date: Tue, 22 Dec 2020 08:43:24 -0500
Subject: [PATCH 1/4] Allow non-coordinate-sorted bam input to eXpress

---
 tools/express/express_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/express/express_wrapper.xml b/tools/express/express_wrapper.xml
index bee4f965..6712f268 100644
--- a/tools/express/express_wrapper.xml
+++ b/tools/express/express_wrapper.xml
@@ -25,7 +25,7 @@
 	</command>
 	<inputs>
 		<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
-		<param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
+		<param format="sam,bam,unsorted.bam,qname_sorted.bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
 		<conditional name="additional_params">
             <param name="use_additional" type="select" label="Use Additional Parameters?">
                 <option value="no">No</option>

From 352e46372cd3bc1078ed3343a8cee3d555489842 Mon Sep 17 00:00:00 2001
From: Gautam Naishadham <gnaishadham@neb.com>
Date: Tue, 29 Dec 2020 06:58:16 -0500
Subject: [PATCH 2/4] Remove (sorted) bam input for eXpress

---
 tools/express/express_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/express/express_wrapper.xml b/tools/express/express_wrapper.xml
index 6712f268..0b164a84 100644
--- a/tools/express/express_wrapper.xml
+++ b/tools/express/express_wrapper.xml
@@ -25,7 +25,7 @@
 	</command>
 	<inputs>
 		<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
-		<param format="sam,bam,unsorted.bam,qname_sorted.bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
+		<param format="sam,unsorted.bam,qname_sorted.bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
 		<conditional name="additional_params">
             <param name="use_additional" type="select" label="Use Additional Parameters?">
                 <option value="no">No</option>

From b5b7756812a33d4d20908af9a1762d2213a0ec77 Mon Sep 17 00:00:00 2001
From: Gautam Naishadham <gnaishadham@neb.com>
Date: Tue, 29 Dec 2020 10:38:08 -0500
Subject: [PATCH 3/4] Remove redundant dependencies file for eXpress

---
 tools/express/tool_dependencies.xml | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 tools/express/tool_dependencies.xml

diff --git a/tools/express/tool_dependencies.xml b/tools/express/tool_dependencies.xml
deleted file mode 100644
index 4d6a67e1..00000000
--- a/tools/express/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="eXpress" version="1.1.1">
-      <repository name="package_express_1_1_1" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>

From 0860a87a70e0e540382bf8345d5e1b2c832b75e1 Mon Sep 17 00:00:00 2001
From: Gautam Naishadham <gnaishadham@neb.com>
Date: Tue, 29 Dec 2020 10:38:22 -0500
Subject: [PATCH 4/4] Upgrade eXpress to version 1.5.1

---
 tools/express/express_wrapper.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/express/express_wrapper.xml b/tools/express/express_wrapper.xml
index 0b164a84..8263b263 100644
--- a/tools/express/express_wrapper.xml
+++ b/tools/express/express_wrapper.xml
@@ -1,7 +1,7 @@
-<tool id="express" name="eXpress" version="1.1.1">
+<tool id="express" name="eXpress" version="1.5.1">
 	<description>Quantify the abundances of a set of target sequences from sampled subsequences</description>
 	<requirements>
-		<requirement type="package" version="1.1.1">eXpress</requirement>
+		<requirement type="package" version="1.5.1">eXpress</requirement>
 	</requirements>
 	<command>
 		express --no-update-check