# HG changeset patch
# User ebi-gxa
# Date 1587029596 0
# Node ID 885d08cc78ad1f2004cd8107a1366e5b7201aeef
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
diff -r 000000000000 -r 885d08cc78ad seurat_find_neighbours.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_find_neighbours.xml Thu Apr 16 09:33:16 2020 +0000
@@ -0,0 +1,128 @@
+
+ constructs a Shared Nearest Neighbor (SNN) Graph
+
+ seurat_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ do_plot
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 885d08cc78ad seurat_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_macros.xml Thu Apr 16 09:33:16 2020 +0000
@@ -0,0 +1,127 @@
+
+
+ 0.0.6
+ 3.1.1
+
+
+ seurat-scripts
+
+
+
+ /dev/null | grep -v -i "WARNING: ")
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ #if $input.format == "anndata"
+ --input-object-file '$input.anndata_file' --input-format anndata
+ #else if $input.format == "loom"
+ --input-object-file '$input.loom_file' --input-format loom
+ #else if $input.format == "rds_seurat"
+ --input-object-file '$input.rds_seurat_file' --input-format seurat
+ #else if $input.format == "rds_sce"
+ --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+ format == 'loom'
+
+
+ format == 'rds_seurat'
+
+
+ format == 'rds_sce'
+
+
+
+
+ #if $format == "anndata"
+ --output-object-file '$anndata_file' --output-format anndata
+ #else if $format == "loom"
+ --output-object-file seurat_obj.loom --output-format loom
+ #else if $format == "rds_seurat"
+ --output-object-file '$rds_seurat_file' --output-format seurat
+ #else if $format == "rds_sce"
+ --output-object-file '$rds_sce_file' --output-format singlecellexperiment
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/nbt.4096
+
+ @misc{r-seurat-scripts.git,
+ author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
+ year = {2018},
+ title = {Seurat-scripts: command line interface for Seurat},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
+ }
+
+ 10.1101/2020.04.08.032698
+
+
+