diff --git a/tools/celesta/celesta.xml b/tools/celesta/celesta.xml index 158a447..06b9b7f 100644 --- a/tools/celesta/celesta.xml +++ b/tools/celesta/celesta.xml @@ -22,7 +22,6 @@ --lowfilter '$low_threshold' --highfilter '$high_threshold' #end if - && #else if str($runmode.selected_mode) == 'assign_cells': Rscript '$__tool_directory__/celesta_assign_cells.R' --imagingdata '$anndata' @@ -42,22 +41,16 @@ #if $high_thresholds_file: --highexpthresh '$high_thresholds_file' #end if - && #for $p in $plot_cells: - Rscript '$__tool_directory__/celesta_plot_cells.R' + && Rscript '$__tool_directory__/celesta_plot_cells.R' --prior '$prior_info' --celltypes '${p.cell_types}' --size '$p.test_size' --height '$p.height' --width '$p.width' --dpi '$p.dpi' - && #end for #end if - - ##final command to satisfy double ampersands - echo 'CELESTA' $runmode.selected_mode 'complete' - ]]>