From fdb3fca289f9651b6dcc22ee72a9eb4435015725 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Sat, 29 Apr 2023 15:37:14 +0100
Subject: [PATCH 1/3] Update sceasy_macros.xml to 0.0.7

---
 tools/tertiary-analysis/sceasy/sceasy_macros.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/tertiary-analysis/sceasy/sceasy_macros.xml b/tools/tertiary-analysis/sceasy/sceasy_macros.xml
index 23ddce74..b3dc6358 100644
--- a/tools/tertiary-analysis/sceasy/sceasy_macros.xml
+++ b/tools/tertiary-analysis/sceasy/sceasy_macros.xml
@@ -1,15 +1,16 @@
 <macros>
-  <token name="@TOOL_VERSION@">0.0.5</token>
+  <token name="@TOOL_VERSION@">0.0.7</token>
   <token name="@HELP@">More information can be found at https://github.com/cellgeni/sceasy</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+0.0.7+galaxy0: Moves to SCEasy 0.0.7
 
 0.0.1+galaxy0: Initial version based on sceasy 0.0.5 by Ni Huang, WTSI.
     ]]></token>
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.0.5">r-sceasy</requirement>
+      <requirement type="package" version="0.0.7">r-sceasy</requirement>
       <yield/>
     </requirements>
   </xml>

From 508f602505ab075ba423f317f80db2982a46f101 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Sat, 29 Apr 2023 15:39:06 +0100
Subject: [PATCH 2/3] Set to galaxy0

---
 tools/tertiary-analysis/sceasy/sceasy_convert.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/tertiary-analysis/sceasy/sceasy_convert.xml b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
index 2d44a6c8..e2efdf18 100644
--- a/tools/tertiary-analysis/sceasy/sceasy_convert.xml
+++ b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy1">
+<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy0">
   <description>a data object between formats</description>
   <macros>
     <import>sceasy_macros.xml</import>

From 199f45c2503eb3e40371d6881379a61d297a96d5 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Sat, 29 Apr 2023 18:41:59 +0000
Subject: [PATCH 3/3] Adds test-data and tests

---
 .../tertiary-analysis/sceasy/get_test_data.sh | 26 +++++++++++++++++++
 .../sceasy/sceasy_convert.xml                 | 21 ++++++++++++---
 2 files changed, 44 insertions(+), 3 deletions(-)
 create mode 100755 tools/tertiary-analysis/sceasy/get_test_data.sh

diff --git a/tools/tertiary-analysis/sceasy/get_test_data.sh b/tools/tertiary-analysis/sceasy/get_test_data.sh
new file mode 100755
index 00000000..7d96f884
--- /dev/null
+++ b/tools/tertiary-analysis/sceasy/get_test_data.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+mkdir -p test-data
+
+BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
+
+LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
+SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
+H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
+RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
+
+function get_data {
+  local link=$1
+  local fname=$2
+
+  if [ ! -f $fname ]; then
+    echo "$fname not available locally, downloading.."
+    wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
+  fi
+}
+
+pushd test-data
+get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
+get_data $RDS_LINK $BASENAME_FILE".rds"
+get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
+get_data $H5AD_LINK $BASENAME_FILE".h5ad"
\ No newline at end of file
diff --git a/tools/tertiary-analysis/sceasy/sceasy_convert.xml b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
index e2efdf18..b7297852 100644
--- a/tools/tertiary-analysis/sceasy/sceasy_convert.xml
+++ b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
@@ -84,7 +84,7 @@
     <data name="output_loom" format="h5" from_work_dir="output.loom" label="${tool.name} on ${on_string}: Loom">
       <filter>conversion['direction'].endswith('loom')</filter>
     </data>
-    <data name="output_anndata" format="h5" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
+    <data name="output_anndata" format="h5ad" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
       <filter>conversion['direction'].endswith('anndata')</filter>
     </data>
   </outputs>
@@ -92,8 +92,23 @@
   <tests>
     <test>
       <param name="direction" value="loom2sce"/>
-      <param name="input_object_file" value="input.loom"/>
-      <output name="output_sce" file="output.rds" ftype="rdata" compare="sim_size"/>
+      <param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_loom.h5"/>
+      <output name="output_sce" file="E-MTAB-6077-3k_features_90_cells_sce.rds" ftype="rdata" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="direction" value="sce2loom"/>
+      <param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds"/>
+      <output name="output_sce" file="E-MTAB-6077-3k_features_90_cells_loom.h5" ftype="h5" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="direction" value="sce2anndata"/>
+      <param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds"/>
+      <output name="output_sce" file="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5" compare="sim_size"/>
+    </test>
+    <test>
+      <param name="direction" value="seurat2anndata"/>
+      <param name="input_object_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
+      <output name="output_sce" file="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad" compare="sim_size"/>
     </test>
   </tests>