# HG changeset patch
# User ebi-gxa
# Date 1574710732 18000
# Node ID 6eb7a2e37adfe134479ab6ae80a103e471230ed5
# Parent 3bd1152dd8547b8a0d4f3830ca03b27f038645e1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
diff -r 3bd1152dd854 -r 6eb7a2e37adf scanpy-filter-genes.xml.bak
--- a/scanpy-filter-genes.xml.bak Wed Nov 20 05:16:20 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
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- based on counts and numbers of cells expressed
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- scanpy_macros2.xml
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diff -r 3bd1152dd854 -r 6eb7a2e37adf scanpy-run-umap.xml
--- a/scanpy-run-umap.xml Wed Nov 20 05:16:20 2019 -0500
+++ b/scanpy-run-umap.xml Mon Nov 25 14:38:52 2019 -0500
@@ -1,5 +1,5 @@
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visualise cell clusters using UMAP
scanpy_macros2.xml
@@ -64,7 +64,7 @@
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embeddings
diff -r 3bd1152dd854 -r 6eb7a2e37adf scanpy_macros2.xml
--- a/scanpy_macros2.xml Wed Nov 20 05:16:20 2019 -0500
+++ b/scanpy_macros2.xml Mon Nov 25 14:38:52 2019 -0500
@@ -4,6 +4,8 @@
=1.4.2).
@@ -17,7 +19,11 @@
--input-format '${input_format}' input.h5
- --show-obj stdout --output-format '${output_format}' output.h5
+#if str($output_format).startswith('anndata')
+ --show-obj stdout --output-format anndata output.h5
+#else
+ --show-obj stdout --output-format loom output.h5
+#end if
#if $fig_title
@@ -33,7 +39,7 @@
- scanpy-scripts
+ scanpy-scripts
@@ -55,7 +61,7 @@
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@@ -64,11 +70,44 @@
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+ output_format == 'anndata_h5ad'
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+ output_format == 'anndata'
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+ output_format == 'anndata_h5ad'
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+ output_format == 'anndata'
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+ output_format == 'loom_legacy'
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+ output_format == 'loom'
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