# HG changeset patch
# User ebi-gxa
# Date 1574680051 18000
# Node ID 4fff8ad1c76d7a0a9b2f0fecb5615a046257056f
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
diff -r 000000000000 -r 4fff8ad1c76d README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Mon Nov 25 06:07:31 2019 -0500
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+Seurat tools
diff -r 000000000000 -r 4fff8ad1c76d seurat_find_neighbours.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_find_neighbours.xml Mon Nov 25 06:07:31 2019 -0500
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+ constructs a Shared Nearest Neighbor (SNN) Graph
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+ seurat_macros.xml
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+ do_plot
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diff -r 000000000000 -r 4fff8ad1c76d seurat_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_macros.xml Mon Nov 25 06:07:31 2019 -0500
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+ 0.0.6
+ 3.1.1
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+ seurat-scripts
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+ /dev/null | grep -v -i "WARNING: ")
+ ]]>
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+ #if $input.format == "anndata"
+ --input-object-file '$input.anndata_file' --input-format anndata
+ #else if $input.format == "loom"
+ --input-object-file '$input.loom_file' --input-format loom
+ #else if $input.format == "rds_seurat"
+ --input-object-file '$input.rds_seurat_file' --input-format seurat
+ #else if $input.format == "rds_sce"
+ --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
+ #end if
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+ format == 'loom'
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+ format == 'rds_seurat'
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+ format == 'rds_sce'
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+ #if $format == "anndata"
+ --output-object-file '$anndata_file' --output-format anndata
+ #else if $format == "loom"
+ --output-object-file seurat_obj.loom --output-format loom
+ #else if $format == "rds_seurat"
+ --output-object-file '$rds_seurat_file' --output-format seurat
+ #else if $format == "rds_sce"
+ --output-object-file '$rds_sce_file' --output-format singlecellexperiment
+ #end if
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+ 10.1038/nbt.4096
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+ @misc{r-seurat-scripts.git,
+ author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
+ year = {2018},
+ title = {Seurat-scripts: command line interface for Seurat},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
+ }
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