diff get_test_data.sh @ 0:77d680b36e23 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Fri Mar 15 12:17:49 2024 +0000
@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+
+BASENAME_FILE='mito_counted_anndata.h5ad'
+
+MTX_LINK='https://zenodo.org/record/7053673/files/Mito-counted_AnnData'
+
+# convenience for getting data
+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
+}
+
+# get matrix data
+mkdir -p test-data
+pushd test-data
+get_data $MTX_LINK $BASENAME_FILE
+
+
+# Download input anndata for decoupler-pathway_inference
+BASENAME_FILE='pbmc3k_processed.h5ad'
+
+MTX_LINK='https://zenodo.org/records/3752813/files/pbmc3k_processed.h5ad'
+
+get_data $MTX_LINK $BASENAME_FILE
+
+# Download output anndata for decoupler-pathway_inference
+BASENAME_FILE='test.h5ad'
+
+MTX_LINK='https://zenodo.org/records/10401958/files/test.h5ad'
+
+get_data $MTX_LINK $BASENAME_FILE
+