# HG changeset patch
# User ebi-gxa
# Date 1626987432 0
# Node ID 9f8381c5d80838d72864b11c35fb39876ca359da
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
diff -r 000000000000 -r 9f8381c5d808 scanpy-multiplet-scrublet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-multiplet-scrublet.xml Thu Jul 22 20:57:12 2021 +0000
@@ -0,0 +1,121 @@
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+ remove multiplets from annData objects with Scrublet
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+ scanpy_macros2.xml
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diff -r 000000000000 -r 9f8381c5d808 scanpy_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros.xml Thu Jul 22 20:57:12 2021 +0000
@@ -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
+
+
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+ scanpy-scripts
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+ ${export_mtx}
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+ 10.1186/s13059-017-1382-0
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+ @misc{githubscanpy-scripts,
+ author = {Ni Huang, EBI Gene Expression Team},
+ year = {2018},
+ title = {Scanpy-scripts: command line interface for Scanpy},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
+ }
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+ export_mtx
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+ export_mtx
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+ export_mtx
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diff -r 000000000000 -r 9f8381c5d808 scanpy_macros2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml Thu Jul 22 20:57:12 2021 +0000
@@ -0,0 +1,166 @@
+
+ 1.8.1
+ More information can be found at https://scanpy.readthedocs.io
+ 18.01
+ =1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+ ]]>
+
+ --input-format '${input_format}' input.h5
+
+
+ #if $save_raw
+ --save-raw
+ #end if
+ #if $save_layer
+ --save-layer ${settings.save_layer}
+ #end if
+
+
+#if str($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}
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+ scanpy-scripts
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+ 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},
+ }
+ 10.1101/2020.04.08.032698
+ 10.1038/s41592-021-01102-w
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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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+ export_mtx
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+ export_mtx
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+ export_mtx
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+