# HG changeset patch
# User ebi-gxa
# Date 1584004221 0
# Node ID a13cc1d401b7d290153e5d0493c63530e22482de
# Parent 81db17245979dc2920e0fade82a1855e3da99741
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
diff -r 81db17245979 -r a13cc1d401b7 scanpy_macros.xml
--- a/scanpy_macros.xml Wed Mar 20 12:00:08 2019 -0400
+++ b/scanpy_macros.xml Thu Mar 12 09:10:21 2020 +0000
@@ -38,9 +38,14 @@
+
+ ${export_mtx}
+
@@ -87,4 +92,18 @@
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+ export_mtx
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+ export_mtx
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+ export_mtx
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+
diff -r 81db17245979 -r a13cc1d401b7 scanpy_macros2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml Thu Mar 12 09:10:21 2020 +0000
@@ -0,0 +1,142 @@
+
+ 1.4.3
+ More information can be found at https://scanpy.readthedocs.io
+ 18.01
+ =1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+ ]]>
+
+ --input-format '${input_format}' input.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 $fig_title
+ --title '${fig_title}'
+#end if
+ --fig-size '${fig_size}'
+ --fig-dpi ${fig_dpi}
+ --fig-fontsize ${fig_fontsize}
+ ${fig_frame}
+ ./output.png
+
+ ${export_mtx}
+
+
+
+ scanpy-scripts
+
+
+
+
+
+
+
+ 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},
+ }
+
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+ output_format == 'anndata_h5ad'
+
+
+ output_format == 'anndata'
+
+
+
+
+
+ output_format == 'anndata_h5ad'
+
+
+ output_format == 'anndata'
+
+
+ output_format == 'loom_legacy'
+
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+ output_format == 'loom'
+
+
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+ export_mtx
+
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+ export_mtx
+
+
+ export_mtx
+
+
+