Merge pull request #88 from goeckslab/celesta-22.01-fix

CELESTA: Fix cheetah variables to work with galaxy-22.01

tools/celesta/celesta.xml

@@ -14,32 +14,32 @@
  --prior '$prior_info'
  --xcol '$x_coord'
  --ycol '$y_coord'
- --size '$test_size' 
- --height '$height' 
- --width '$width' 
+ --size '${runmode.figure_options.test_size}' 
+ --height '${runmode.figure_options.height}' 
+ --width '${runmode.figure_options.width}' 
  #if str($filter_cells.filter) == 'filter':
  --filter
- --lowfilter '$low_threshold'
- --highfilter '$high_threshold'
+ --lowfilter '${filter_cells.low_threshold}'
+ --highfilter '${filter_cells.high_threshold}'
  #end if
  #else if str($runmode.selected_mode) == 'assign_cells':
  Rscript '$__tool_directory__/celesta_assign_cells.R'
  --imagingdata '$anndata'
  --prior '$prior_info'
- --xcol '$x_coord' 
- --ycol '$y_coord' 
- --maxiteration '$max_iteration' 
- --changethresh '$cell_change_threshold' 
+ --xcol '$x_coord'
+ --ycol '$y_coord'
+ --maxiteration '${runmode.options.max_iteration}' 
+ --changethresh '${runmode.options.cell_change_threshold}' 
  #if str($filter_cells.filter) == 'filter':
  --filter
- --lowfilter '$low_threshold'
- --highfilter '$high_threshold'
+ --lowfilter '${filter_cells.low_threshold}'
+ --highfilter '${filter_cells.high_threshold}'
  #end if
- #if $low_thresholds_file:
- --lowexpthresh '$low_thresholds_file'
+ #if $runmode.options.low_thresholds_file:
+ --lowexpthresh '${runmode.options.low_thresholds_file}'
  #end if
- #if $high_thresholds_file:
- --highexpthresh '$high_thresholds_file'
+ #if $runmode.options.high_thresholds_file:
+ --highexpthresh '${runmode.options.high_thresholds_file}'
  #end if 
  #for $p in $plot_cells:
  && Rscript '$__tool_directory__/celesta_plot_cells.R'
@@ -59,21 +59,33 @@
  <inputs>
  <param name="anndata" type="data" format="h5ad" label="Input anndata" />
  <param name="prior_info" type="data" format="csv" label="Cell-type signature matrix" />
+ <param name="x_coord" type="text" value="X_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid X position" />
+ <param name="y_coord" type="text" value="Y_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid Y position" />
+ <conditional name="filter_cells">
+ <param name="filter" type="select" label="Choose whether to filter cells" help="FilterCells">
+ <option value="no_filter" selected="true">Do not filter cells</option>
+ <option value="filter">Filter cells based on marker intensity</option>
+ </param>
+ <when value="no_filter">
+ </when>
+ <when value="filter">
+ <param name="low_threshold" type="float" value="0.4" optional="false" label="Set the low threshold for filtering cells" help="Cells below low threshold will be filtered out" />
+ <param name="high_threshold" type="float" value="0.9" optional="false" label="Set the high threshold for filtering cells" help="Cells above high threshold will be filtered out" />
+ </when>
+ </conditional>
  <conditional name="runmode">
  <param name="selected_mode" type="select" label="Select which CELESTA mode to run">
  <option value="plot_expression" selected="true">Plot expression probabilities for markers in the cell type signature matrix</option>
  <option value="assign_cells">Run the cell type assignment</option>
  </param>
  <when value="plot_expression">
- <expand macro="celesta_base_options" />
  <section name="figure_options" title="Figure Options" expanded="true">
  <param argument="test_size" type="float" value="1" min="0.1" max="10" label="Specify the point size for plotting cells" />
  <param argument="height" type="integer" value="4" min="4" max="20" label="Specify the height of the figure (inches)" />
  <param argument="width" type="integer" value="5" min="4" max="20" label="Specify the width of the figure (inches)" />
  </section>
  </when>
  <when value="assign_cells">
- <expand macro="celesta_base_options" />
  <section name="options" title="Advanced Options" expanded="false">
  <param argument="max_iteration" type="integer" value="10" label="Define the maximum iterations allowed in the EM algorithm per round" />
  <param argument="cell_change_threshold" type="float" value="0.01" label="Define an ending condition for the EM algorithm" help="0.01 means that when fewer than 1% of the total number of cells do not change identity, the algorithm will stop" />

tools/celesta/macros.xml

@@ -1,6 +1,6 @@
 <macros>
  <token name="@TOOL_VERSION@">0.0.0.9</token>
- <token name="@VERSION_SUFFIX@">0</token>
+ <token name="@VERSION_SUFFIX@">1</token>
  <token name="@PROFILE@">20.01</token>
 
  <xml name="celesta_requirements">
@@ -20,20 +20,4 @@
  <citation type="doi">10.1038/s41592-022-01498-z</citation>
  </citations>
  </xml>
- <xml name="celesta_base_options" token_label="celesta_base_options">
- <param name="x_coord" type="text" value="X_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid X position" />
- <param name="y_coord" type="text" value="Y_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid Y position" />
- <conditional name="filter_cells">
- <param name="filter" type="select" label="Choose whether to filter cells" help="FilterCells">
- <option value="no_filter" selected="true">Do not filter cells</option>
- <option value="filter">Filter cells based on marker intensity</option>
- </param>
- <when value="no_filter">
- </when>
- <when value="filter">
- <param name="low_threshold" type="float" value="0.4" optional="false" label="Set the low threshold for filtering cells" help="Cells below low threshold will be filtered out" />
- <param name="high_threshold" type="float" value="0.9" optional="false" label="Set the high threshold for filtering cells" help="Cells above high threshold will be filtered out" />
- </when>
- </conditional>
- </xml>
 </macros>