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remove hacky && fix from command block
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CameronFRWatson committed Aug 27, 2024
1 parent 3bc9ba7 commit c869b2a
Showing 1 changed file with 1 addition and 8 deletions.
9 changes: 1 addition & 8 deletions tools/celesta/celesta.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand All @@ -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'
]]>
</command>
<configfiles>
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