# HG changeset patch
# User iuc
# Date 1520116456 18000
# Node ID e01c989c75430d3fe00c0f398a92aab715287828
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
diff -r 000000000000 -r e01c989c7543 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Mar 03 17:34:16 2018 -0500
@@ -0,0 +1,37 @@
+
+
+
+
+ 10.1038/nature14966
+
+
+
+
+ r
+ r-tsne
+ r-pheatmap
+ r-mass
+ r-mclust
+ r-flexmix
+ r-lattice
+ r-fpc
+ r-rcolorbrewer
+ r-permute
+ r-amap
+ r-locfit
+
+
+ 1.0
+ $__tool_directory__/scripts
+
+
+ out_rdat_filter.rds
+ out_rdat_kmeans.rds
+ out_rdat_outlier.rds
+
+
+
+ out_rdat_filter.rds
+ out_rdat_kmeans.rds
+ out_rdat_outlier.rds
+
diff -r 000000000000 -r e01c989c7543 raceid_main.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/raceid_main.xml Sat Mar 03 17:34:16 2018 -0500
@@ -0,0 +1,404 @@
+
+ Race ID pipeline for single-cell RNA analysis
+
+ macros.xml
+
+
+
+
+
+ RaceID k-means
+ Gap statistic
+ ![](plot_gap.svg)
+ Jaccard Similarity
+ ![](plot_jaccard.svg)
+ Silhouette Plot
+ ![](plot_silhouette.svg)
+ Cluster Heatmap
+ ![](plot_clustheatmap.svg)
+ ' > '$out_html' &&
+
+ ## Outlier -- relies on kmeans
+ echo "Outlier" &&
+ Rscript '@SCRIPT_DIR@/raceID_outlierdetect.R' '@SCRIPT_DIR@' '$rconf_source_outlier' &&
+
+ mv plot_*.svg '${out_html.files_path}' &&
+ echo '
+
+ RaceID Outlier Detection
+ Background
+ ![](plot_background.svg)
+ Sensitivity
+ ![](plot_sensitivity.svg)
+ Outlier Probability
+ ![](plot_outlierprobs.svg)
+ Final Heatmap
+ ![](plot_finalheat.svg)
+ ' >> '$out_html' &&
+
+ ## tSNE -- relies on kmeans and outlier
+ echo "tSNE" &&
+ Rscript '@SCRIPT_DIR@/raceID_tsne.R' '@SCRIPT_DIR@' '$rconf_source_tsne' &&
+
+ ##mkdir '${out_html.files_path}' &&
+ mv plot_*.svg '${out_html.files_path}' &&
+
+ echo '
+
+ RaceID tSNE
+ Initial k-means clusters
+
+ Final clusters
+
+ Labelled
+
+ Symbols
+
+ ' >> '$out_html' &&
+
+ #if $section_tsne.genexp_select.use_gexpr == "Yes":
+ #for $gene_set in $section_tsne.genexp_select.geneset:
+ echo "Expression for: [${gene_set.genes.value}]
" >> '$out_html' &&
+ echo "
" >> '$out_html' &&
+ #end for
+ #end if
+ echo '