# HG changeset patch
# User ebi-gxa
# Date 1554304325 14400
# Node ID 305d0cbe0ffd1a04e831008cac09dc2eaedff6c8
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
diff -r 000000000000 -r 305d0cbe0ffd scanpy-find-variable-genes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-find-variable-genes.xml Wed Apr 03 11:12:05 2019 -0400
@@ -0,0 +1,93 @@
+
+
+ based on normalised dispersion of expression
+
+ scanpy_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/nbt.3192
+ 10.1038/ncomms14049
+
+
diff -r 000000000000 -r 305d0cbe0ffd scanpy_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros.xml Wed Apr 03 11:12:05 2019 -0400
@@ -0,0 +1,109 @@
+
+ 1.3.2
+ More information can be found at https://scanpy.readthedocs.io
+
+#if $do_plotting.plot
+ -P output.png
+ --projectio $do_plotting.projection
+ --components $do_plotting.components
+ #if $do_plotting.color_by
+ --color-by $do_plotting.color_by
+ #end if
+ #if $do_plotting.groups
+ --group $do_plotting.groups
+ #end if
+ #if $do_plotting.use_raw
+ --use-raw
+ #end if
+ #if $do_plotting.palette
+ --palette $do_plotting.palette
+ #end if
+ #if $do_plotting.edges
+ --edges
+ #end if
+ #if $do_plotting.arrows
+ --arrows
+ #end if
+ #if not $do_plotting.sort_order
+ --no-sort-order
+ #end if
+ #if $do_plotting.frameoff
+ --frameoff
+ #end if
+#end if
+
+
+
+ scanpy-scripts
+
+
+
+
+ ${export_mtx}
+
+
+
+
+ 10.1186/s13059-017-1382-0
+
+ @misc{githubscanpy-scripts,
+ author = {Ni Huang, EBI Gene Expression Team},
+ year = {2018},
+ title = {Scanpy-scripts: command line interface for Scanpy},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ export_mtx
+
+
+ export_mtx
+
+
+ export_mtx
+
+
+