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refactors recent superdsm changes using select param
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@kostrykin
kostrykin committed Nov 15, 2023
1 parent 61f6539 commit eb88a15
Showing 1 changed file with 69 additions and 99 deletions.
168 changes: 69 additions & 99 deletions tools/superdsm/superdsm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,70 +20,65 @@
</requirements>
<command detect_errors="aggressive">
<![CDATA[
#if $do_masks_enabled == 'true' or $do_cfg_enabled == 'true' or $do_overlay.do_overlay_enabled == 'true':
python '$__tool_directory__/run-superdsm.py'
'${dataset}'
\${GALAXY_SLOTS:-4}
#if $do_masks_enabled == 'true':
--do-masks 'masks.png'
#end if
#if $do_cfg_enabled == 'true':
--do-cfg 'cfg.tsv'
#end if
#if $do_overlay.do_overlay_enabled == 'true':
--do-overlay 'overlay.png'
#if $seg_border.value % 2 == 1:
#set $seg_border = "%d" % ($seg_border.value + 1)
--do-overlay-border $seg_border
#else:
--do-overlay-border $seg_border
#end if
#end if
#if str($config.AF_scale) != '':
--AF_scale '${config.AF_scale}'
#end if
#if str($config.c2f_region_analysis_min_atom_radius) != '':
--c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
#end if
#if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
--c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
#end if
#if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
--c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
#end if
#if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
--c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
#end if
#if str($config.dsm_alpha) != '':
--dsm_alpha '${config.dsm_alpha}'
#end if
#if str($config.dsm_AF_alpha) != '':
--dsm_AF_alpha '${config.dsm_AF_alpha}'
#end if
#if str($config.global_energy_minimization_beta) != '':
--global_energy_minimization_beta '${config.global_energy_minimization_beta}'
#end if
#if str($config.global_energy_minimization_AF_beta) != '':
--global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
#end if
#if str($config.postprocess_mask_max_distance) != '':
--postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
#end if
#if str($config.postprocess_mask_stdamp) != '':
--postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
#end if
#if str($config.postprocess_max_norm_energy) != '':
--postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
#end if
#if str($config.postprocess_min_contrast) != '':
--postprocess_min_contrast '${config.postprocess_min_contrast}'
#end if
#if str($config.postprocess_min_object_radius) != '':
--postprocess_min_object_radius '${config.postprocess_min_object_radius}'
python '$__tool_directory__/run-superdsm.py'
'${dataset}'
\${GALAXY_SLOTS:-4}
#if 'masks' in $outputs:
--do-masks 'masks.png'
#end if
#if 'cfg' in $outputs:
--do-cfg 'cfg.tsv'
#end if
#if 'overlay' in $outputs:
--do-overlay 'overlay.png'
#if $seg_border.value % 2 == 1:
#set $seg_border = "%d" % ($seg_border.value + 1)
--do-overlay-border $seg_border
#else:
--do-overlay-border $seg_border
#end if
#else
echo "No outputs selected."
exit 1
#end if
#if str($config.AF_scale) != '':
--AF_scale '${config.AF_scale}'
#end if
#if str($config.c2f_region_analysis_min_atom_radius) != '':
--c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
#end if
#if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
--c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
#end if
#if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
--c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
#end if
#if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
--c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
#end if
#if str($config.dsm_alpha) != '':
--dsm_alpha '${config.dsm_alpha}'
#end if
#if str($config.dsm_AF_alpha) != '':
--dsm_AF_alpha '${config.dsm_AF_alpha}'
#end if
#if str($config.global_energy_minimization_beta) != '':
--global_energy_minimization_beta '${config.global_energy_minimization_beta}'
#end if
#if str($config.global_energy_minimization_AF_beta) != '':
--global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
#end if
#if str($config.postprocess_mask_max_distance) != '':
--postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
#end if
#if str($config.postprocess_mask_stdamp) != '':
--postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
#end if
#if str($config.postprocess_max_norm_energy) != '':
--postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
#end if
#if str($config.postprocess_min_contrast) != '':
--postprocess_min_contrast '${config.postprocess_min_contrast}'
#end if
#if str($config.postprocess_min_object_radius) != '':
--postprocess_min_object_radius '${config.postprocess_min_object_radius}'
#end if
]]>
</command>
Expand All @@ -92,27 +87,12 @@
</environment_variables>
<inputs>
<param name="dataset" type="data" format="tiff,png" label="Dataset" />
<section name="outputs" title="Outputs" expanded="true">
<conditional name="do_overlay">
<param name="do_overlay_enabled" type="select" label="Segmentation overlay">
<option value="true" selected="true">Create a segmentation overlay</option>
<option value="false">Do not create a segmentation overlay</option>
</param>
<when value="true">
<param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" />
</when>
<when value="false">
</when>
</conditional>
<param name="do_masks_enabled" type="select" label="Label map">
<option value="true">Create a label map (e.g., for further processing)</option>
<option value="false" selected="true">Do not create a label map</option>
</param>
<param name="do_cfg_enabled" type="select" label="Hyperparameters">
<option value="true">Report all hyperparameters (manually set and automatically determined values)</option>
<option value="false" selected="true">Do not report the values of the hyperparamters</option>
</param>
</section>
<param name="outputs" type="select" label="Outputs" multiple="true" optional="false">
<option value="overlay" selected="true">Create a segmentation overlay</option>
<option value="masks">Create a label map (e.g., for further processing)</option>
<option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
</param>
<param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" help="This parameter is only used for segmentation overlays (see above)." />
<section name="config" title="Hyperparameters" expanded="false">
<param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale σ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." />
<param argument="--c2f_region_analysis_min_atom_radius" optional="true" type="float" value="" min="0" label="min_atom_radius" help="No region determined by the Coarse-to-fine region analysis scheme is smaller than a circle of this radius (in terms of the surface area). Leave empty to use the automatically determined value." />
Expand All @@ -132,37 +112,27 @@
</inputs>
<outputs>
<data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
<filter>outputs['do_masks_enabled'] == 'true'</filter>
<filter>'masks' in outputs</filter>
</data>
<data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
<filter>outputs['do_cfg_enabled'] == 'true'</filter>
<filter>'cfg' in outputs</filter>
</data>
<data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
<filter>outputs['do_overlay']['do_overlay_enabled'] == 'true'</filter>
<filter>'overlay' in outputs</filter>
</data>
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="dataset" value="BBBC033_C2_z28.png" />
<param name="do_masks_enabled" value="true" />
<param name="do_overlay_enabled" value="true" />
<param name="do_cfg_enabled" value="true" />
<param name="outputs" value="overlay,masks,cfg" />
<output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
<output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
</test>
<test expect_num_outputs="1">
<param name="dataset" value="BBBC033_C2_z28.png" />
<param name="do_masks_enabled" value="false" />
<param name="do_overlay_enabled" value="false" />
<param name="do_cfg_enabled" value="true" />
<param name="outputs" value="cfg" />
<output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
</test>
<test expect_failure="true">
<param name="dataset" value="BBBC033_C2_z28.png" />
<param name="do_masks_enabled" value="false" />
<param name="do_overlay_enabled" value="false" />
<param name="do_cfg_enabled" value="false" />
</test>
</tests>
<help>
This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
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