# HG changeset patch
# User ebi-gxa
# Date 1587028790 0
# Node ID d930c32e932b6740a4c5e2ad9b94a7eb4645ca8d
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 3fc448754d6720855f781caa7938e33d3961b092"
diff -r 000000000000 -r d930c32e932b run_sccaf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/run_sccaf.xml Thu Apr 16 09:19:50 2020 +0000
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+
+
+ to assess and optimise clustering
+
+ sccaf_macros.xml
+
+
+ ${opt_text_out};
+#end if
+
+#if $mode.optimise and $mode.distribute_assesment:
+mkdir -p outputs;
+for round in \$(cat rounds.txt); do
+ echo "Round: "\$round;
+ echo \$round > outputs/round_\$round\.txt;
+done
+#end if
+
+
+
+]]>
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+ not mode['skip_init_assessment']
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+ mode['optimise']
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+ mode['optimise']
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+ mode['optimise'] and mode['distribute_assesment']
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+ mode['optimise']
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+ mode['optimise']
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diff -r 000000000000 -r d930c32e932b sccaf_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sccaf_macros.xml Thu Apr 16 09:19:50 2020 +0000
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+
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+ sccaf
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+ 0.0.9
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+SCCAF explained
+===============
+
+Single Cell Clustering Assessment Framework (SCCAF) is a novel method for
+automated identification of putative cell types from single cell RNA-seq
+(scRNA-seq) data. By iteratively applying clustering and a machine learning
+approach to gene expression profiles of a given set of cells, SCCAF
+simultaneously identifies distinct cell groups and a weighted list of feature
+genes for each group. The feature genes, which are overexpressed in the
+particular cell group, jointly discriminate the given cell group from other
+cells. Each such group of cells corresponds to a putative cell type or state,
+characterised by the feature genes as markers.
+
+ More information can be found at https://github.com/SCCAF/SCCAF
+
+ #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.show_edges
+ --edges
+ #end if
+ #if $do_plotting.show_arrows
+ --arrows
+ #end if
+ #if not $do_plotting.color_order
+ --no-sort-order
+ #end if
+ #if $do_plotting.omit_frame
+ --frameoff
+ #end if
+#end if
+
+
+
+
+
+ @misc{githubsccaf,
+ author = {Miao, Zhichao},
+ year = {2018},
+ title = {SCCAF},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/Functional-Genomics/SCCAF},
+ }
+ 10.1101/2020.04.08.032698
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+ output_format == 'anndata_h5ad'
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+ output_format == 'anndata'
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diff -r 000000000000 -r d930c32e932b static/images/example_sccaf_workflow.png
Binary file static/images/example_sccaf_workflow.png has changed