# HG changeset patch
# User ebi-gxa
# Date 1646378858 0
# Node ID 8d9ceaec2c7f4fc12a8de5a0280cf9fe6da1706c
# Parent 2d294978b15214e588f7b41401ce4383641584f6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
diff -r 2d294978b152 -r 8d9ceaec2c7f get_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh Fri Mar 04 07:27:38 2022 +0000
@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
+
+MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
+RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
+NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
+FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
+SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
+PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
+NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
+CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
+TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
+MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
+
+LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
+H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
+SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
+
+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
+pushd test-data
+get_data $MTX_LINK mtx.zip
+unzip mtx.zip
+rm -f mtx.zip
+
+get_data $RDS_LINK $BASENAME_FILE".rds"
+get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
+get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
+get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
+get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
+get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
+get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
+get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
+get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
+
+unzip $BASENAME_FILE"-markers.csv.zip"
+rm -f $BASENAME_FILE"-markers.csv.zip"
+
+get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
+get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
+get_data $H5AD_LINK $BASENAME_FILE".h5ad"
diff -r 2d294978b152 -r 8d9ceaec2c7f seurat_macros.xml
--- a/seurat_macros.xml Fri Nov 27 13:49:39 2020 +0000
+++ b/seurat_macros.xml Fri Mar 04 07:27:38 2022 +0000
@@ -1,7 +1,7 @@
- 0.0.8
- 3.1.2
+ 0.3.0
+ 3.2.3
seurat-scripts
@@ -96,7 +96,10 @@
@@ -124,7 +127,7 @@
url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
}
- 10.1101/2020.04.08.032698
+ 10.1038/s41592-021-01102-w
diff -r 2d294978b152 -r 8d9ceaec2c7f seurat_run_tsne.xml
--- a/seurat_run_tsne.xml Fri Nov 27 13:49:39 2020 +0000
+++ b/seurat_run_tsne.xml Fri Mar 04 07:27:38 2022 +0000
@@ -1,4 +1,4 @@
-
+
run t-SNE dimensionality reduction
seurat_macros.xml
@@ -66,8 +66,12 @@
-
-
+
+