# HG changeset patch
# User ebi-gxa
# Date 1574186414 18000
# Node ID 086d850271a2bb694d372554faae60830303788a
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
diff -r 000000000000 -r 086d850271a2 anndata_operations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/anndata_operations.xml Tue Nov 19 13:00:14 2019 -0500
@@ -0,0 +1,102 @@
+
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+ modifies metadata and flags genes
+
+ scanpy_macros2.xml
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+
+
+import scanpy as sc
+import logging
+
+adata = sc.read('input.h5')
+
+gene_name = '${gene_symbols_field}'
+qc_vars = list()
+
+#for $i, $s in enumerate($modifications)
+adata.obs['${s.to_obs}'] = adata.obs['${s.from_obs}']
+#end for
+
+gene_names = getattr(adata.var, gene_name)
+
+#for $i, $flag in enumerate($gene_flags)
+k_cat = gene_names.str.startswith('${flag.startswith}')
+if k_cat.sum() > 0:
+ adata.var['${flag.flag}'] = k_cat
+ qc_vars.append('${flag.flag}')
+else:
+ logging.warning('No genes starting with {} found, skip calculating expression of {} genes'.format('${flag.startswith}', '${flag.flag}'))
+#end for
+
+
+if len(qc_vars) > 0:
+ pct_top = [${top_genes}]
+ sc.pp.calculate_qc_metrics(adata, qc_vars=qc_vars, percent_top=pct_top, inplace=True)
+
+if 'n_genes' not in adata.obs.columns:
+ sc.pp.filter_cells(adata, min_genes=0)
+if 'n_counts' not in adata.obs.columns:
+ sc.pp.filter_cells(adata, min_counts=0)
+if 'n_cells' not in adata.var.columns:
+ sc.pp.filter_genes(adata, min_cells=0)
+if 'n_counts' not in adata.var.columns:
+ sc.pp.filter_genes(adata, min_counts=0)
+
+adata.write('output.h5', compression='gzip')
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+ _counts).
+* Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes.
+* For top genes specified, calculate qc metrics (pct_counts_in_top__genes).
+
+This functionality will probably be added in the future to a larger package.
+]]>
+
+
diff -r 000000000000 -r 086d850271a2 scanpy_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros.xml Tue Nov 19 13:00:14 2019 -0500
@@ -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
+
+
+
+
+ ${export_mtx}
+
+
+
+
+ 10.1186/s13059-017-1382-0
+
+ @misc{githubscanpy-scripts,
+ author = {Ni Huang, EBI Gene Expression Team},
+ year = {2018},
+ title = {Scanpy-scripts: command line interface for Scanpy},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
+ }
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+ export_mtx
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+ export_mtx
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+ export_mtx
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diff -r 000000000000 -r 086d850271a2 scanpy_macros2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml Tue Nov 19 13:00:14 2019 -0500
@@ -0,0 +1,96 @@
+
+ 1.4.3
+ More information can be found at https://scanpy.readthedocs.io
+ =1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+ ]]>
+
+ --input-format '${input_format}' input.h5
+
+
+ --show-obj stdout --output-format '${output_format}' output.h5
+
+
+#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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+ export_mtx
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+ export_mtx
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+ export_mtx
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