rearranging supplementary tables and adjusting scripts accordingly

Author: EngyNasr

bin/extended_data_figure_2.R

@@ -22,7 +22,7 @@ suppressWarnings({
   ## Load input dataset --------------------------------
 
   tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 
   tools_dt <- tools_url |> fread()

bin/extended_data_figure_3.R

@@ -15,7 +15,7 @@ suppressWarnings({
   })
 
 
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   all_tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
 
   workflows_dt <- workflows_url |> fread(sep = "\t")

bin/extended_data_figure_6.R

@@ -17,7 +17,7 @@ suppressWarnings({
   })
 
 
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   all_tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
 
   workflows_dt <- workflows_url |> fread(sep = "\t")

bin/get_data.sh

@@ -15,20 +15,20 @@ wget \
     -O "docs/supplementary/supplementary_table_2.tsv" \
     "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_tools.tsv" 
 
-# Get use cases
+# Get tool suites number of figure 3
 wget \
     -O "docs/supplementary/supplementary_table_3.tsv" \
-    "https://docs.google.com/spreadsheets/d/1fGbDFk5u4vwrjcdN8zWXHEvxkLUYJSx_nbK1XUeSZyk/export?format=tsv"  
+    "https://docs.google.com/spreadsheets/d/1iG7qXbiMUrQsPxVuIXAvDgyrGK9PWyWpxy1IyDCB2TQ/export?format=tsv"  
 
-# Get tool suites number of figure 3
+# Get workflows table
 wget \
     -O "docs/supplementary/supplementary_table_4.tsv" \
-    "https://docs.google.com/spreadsheets/d/1iG7qXbiMUrQsPxVuIXAvDgyrGK9PWyWpxy1IyDCB2TQ/export?format=tsv"  
+    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_workflows.tsv" 
 
-# Get workflows table
+# Get use cases
 wget \
     -O "docs/supplementary/supplementary_table_5.tsv" \
-    "https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/microgalaxy/resources/curated_workflows.tsv" 
+    "https://docs.google.com/spreadsheets/d/1fGbDFk5u4vwrjcdN8zWXHEvxkLUYJSx_nbK1XUeSZyk/export?format=tsv"  
 
 # Get tutorials table
 wget \

bin/helper_figure_3a.R

@@ -18,7 +18,7 @@ library(colorspace, quietly = TRUE)
 
 plot_figure_3A <- function() {
   tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 
   tools_dt <- tools_url |> fread()

bin/helper_figure_3b.R

@@ -13,7 +13,7 @@ library(ggforce, quietly = TRUE)
 
 plot_figure_3B <- function() {
   tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 
   tools_dt <- tools_url |> fread()

bin/helper_figure_3c.R

@@ -15,7 +15,7 @@ library(tidytext, quietly = TRUE)
 
 plot_figure_3C <- function() {
   tools_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_2.tsv"
-  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_5.tsv"
+  workflows_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_4.tsv"
   tutorials_url <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/docs/supplementary/supplementary_table_6.tsv"
 
   tools_dt <- tools_url |> fread()