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comparison celesta.xml @ 1:44d4c885d9b5 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/celesta commit 1f02a762ab43a29aa7f59760798ff084f86e37db
author goeckslab
date Thu, 12 Sep 2024 16:49:51 +0000
parents 8001319743c0
children 41aaffbb9473
comparison
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0:8001319743c0 1:44d4c885d9b5
12 Rscript '$__tool_directory__/celesta_plot_expression.R' 12 Rscript '$__tool_directory__/celesta_plot_expression.R'
13 --imagingdata '$anndata' 13 --imagingdata '$anndata'
14 --prior '$prior_info' 14 --prior '$prior_info'
15 --xcol '$x_coord' 15 --xcol '$x_coord'
16 --ycol '$y_coord' 16 --ycol '$y_coord'
17 --size '$test_size' 17 --size '${runmode.figure_options.test_size}'
18 --height '$height' 18 --height '${runmode.figure_options.height}'
19 --width '$width' 19 --width '${runmode.figure_options.width}'
20 #if str($filter_cells.filter) == 'filter': 20 #if str($filter_cells.filter) == 'filter':
21 --filter 21 --filter
22 --lowfilter '$low_threshold' 22 --lowfilter '${filter_cells.low_threshold}'
23 --highfilter '$high_threshold' 23 --highfilter '${filter_cells.high_threshold}'
24 #end if 24 #end if
25 #else if str($runmode.selected_mode) == 'assign_cells': 25 #else if str($runmode.selected_mode) == 'assign_cells':
26 Rscript '$__tool_directory__/celesta_assign_cells.R' 26 Rscript '$__tool_directory__/celesta_assign_cells.R'
27 --imagingdata '$anndata' 27 --imagingdata '$anndata'
28 --prior '$prior_info' 28 --prior '$prior_info'
29 --xcol '$x_coord' 29 --xcol '$x_coord'
30 --ycol '$y_coord' 30 --ycol '$y_coord'
31 --maxiteration '$max_iteration' 31 --maxiteration '${runmode.options.max_iteration}'
32 --changethresh '$cell_change_threshold' 32 --changethresh '${runmode.options.cell_change_threshold}'
33 #if str($filter_cells.filter) == 'filter': 33 #if str($filter_cells.filter) == 'filter':
34 --filter 34 --filter
35 --lowfilter '$low_threshold' 35 --lowfilter '${filter_cells.low_threshold}'
36 --highfilter '$high_threshold' 36 --highfilter '${filter_cells.high_threshold}'
37 #end if 37 #end if
38 #if $low_thresholds_file: 38 #if $runmode.options.low_thresholds_file:
39 --lowexpthresh '$low_thresholds_file' 39 --lowexpthresh '${runmode.options.low_thresholds_file}'
40 #end if 40 #end if
41 #if $high_thresholds_file: 41 #if $runmode.options.high_thresholds_file:
42 --highexpthresh '$high_thresholds_file' 42 --highexpthresh '${runmode.options.high_thresholds_file}'
43 #end if 43 #end if
44 #for $p in $plot_cells: 44 #for $p in $plot_cells:
45 && Rscript '$__tool_directory__/celesta_plot_cells.R' 45 && Rscript '$__tool_directory__/celesta_plot_cells.R'
46 --prior '$prior_info' 46 --prior '$prior_info'
47 --celltypes '${p.cell_types}' 47 --celltypes '${p.cell_types}'
57 <inputs name="inputs" /> 57 <inputs name="inputs" />
58 </configfiles> 58 </configfiles>
59 <inputs> 59 <inputs>
60 <param name="anndata" type="data" format="h5ad" label="Input anndata" /> 60 <param name="anndata" type="data" format="h5ad" label="Input anndata" />
61 <param name="prior_info" type="data" format="csv" label="Cell-type signature matrix" /> 61 <param name="prior_info" type="data" format="csv" label="Cell-type signature matrix" />
62 <param name="x_coord" type="text" value="X_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid X position" />
63 <param name="y_coord" type="text" value="Y_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid Y position" />
64 <conditional name="filter_cells">
65 <param name="filter" type="select" label="Choose whether to filter cells" help="FilterCells">
66 <option value="no_filter" selected="true">Do not filter cells</option>
67 <option value="filter">Filter cells based on marker intensity</option>
68 </param>
69 <when value="no_filter">
70 </when>
71 <when value="filter">
72 <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" />
73 <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" />
74 </when>
75 </conditional>
62 <conditional name="runmode"> 76 <conditional name="runmode">
63 <param name="selected_mode" type="select" label="Select which CELESTA mode to run"> 77 <param name="selected_mode" type="select" label="Select which CELESTA mode to run">
64 <option value="plot_expression" selected="true">Plot expression probabilities for markers in the cell type signature matrix</option> 78 <option value="plot_expression" selected="true">Plot expression probabilities for markers in the cell type signature matrix</option>
65 <option value="assign_cells">Run the cell type assignment</option> 79 <option value="assign_cells">Run the cell type assignment</option>
66 </param> 80 </param>
67 <when value="plot_expression"> 81 <when value="plot_expression">
68 <expand macro="celesta_base_options" />
69 <section name="figure_options" title="Figure Options" expanded="true"> 82 <section name="figure_options" title="Figure Options" expanded="true">
70 <param argument="test_size" type="float" value="1" min="0.1" max="10" label="Specify the point size for plotting cells" /> 83 <param argument="test_size" type="float" value="1" min="0.1" max="10" label="Specify the point size for plotting cells" />
71 <param argument="height" type="integer" value="4" min="4" max="20" label="Specify the height of the figure (inches)" /> 84 <param argument="height" type="integer" value="4" min="4" max="20" label="Specify the height of the figure (inches)" />
72 <param argument="width" type="integer" value="5" min="4" max="20" label="Specify the width of the figure (inches)" /> 85 <param argument="width" type="integer" value="5" min="4" max="20" label="Specify the width of the figure (inches)" />
73 </section> 86 </section>
74 </when> 87 </when>
75 <when value="assign_cells"> 88 <when value="assign_cells">
76 <expand macro="celesta_base_options" />
77 <section name="options" title="Advanced Options" expanded="false"> 89 <section name="options" title="Advanced Options" expanded="false">
78 <param argument="max_iteration" type="integer" value="10" label="Define the maximum iterations allowed in the EM algorithm per round" /> 90 <param argument="max_iteration" type="integer" value="10" label="Define the maximum iterations allowed in the EM algorithm per round" />
79 <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" /> 91 <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" />
80 <param name="low_thresholds_file" type="data" format="csv" optional="true" label="Provide a file mapping low anchor and index cell assignment thresholds to cell types" /> 92 <param name="low_thresholds_file" type="data" format="csv" optional="true" label="Provide a file mapping low anchor and index cell assignment thresholds to cell types" />
81 <param name="high_thresholds_file" type="data" format="csv" optional="true" label="Provide a file mapping high anchor and index cell assignment thresholds to cell types" /> 93 <param name="high_thresholds_file" type="data" format="csv" optional="true" label="Provide a file mapping high anchor and index cell assignment thresholds to cell types" />