new tool: galaxy wrappers for the pcdl physicell data lader command line commands #7034
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| name: pcdl | ||
| owner: iuc | ||
| description: pcdl PhysiCell Data Loader. | ||
| long_description: Galaxy wrapper for the pcdl PhysiCell Data Loader command line commands for downstream analysis from PhysiCell output. | ||
| homepage_url: https://github.com/elmbeech/physicelldataloader | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ | ||
| type: unrestricted | ||
| categories: [Systems Biology, Data Export, Graphics] | ||
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| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Galaxy wrapper for physicell dataloader function: {{ tool_name }}." | ||
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| suite: | ||
| name: suite_pcdl | ||
| description: Galaxy wrapper suite for the pcdl PhysiCell Data Loader command line commands. | ||
| long_description: Galaxy wrapper suite for the pcdl PhysiCell Data Loader command line commands. Pcdl is paramount for downstream analysis from PhysiCell output. As such, the pcdl Galaxy tools are useful if you work with the interactive PhysiCell Studio Galaxy tool. |
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| pcdl | ||
| ==== | ||
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| Galaxy wrapper for the pcdl PhysiCell Data Loader command line commands. | ||
| Pcdl is paramount for downstream analysis from PhysiCell output. | ||
| As such, the pcdl Galaxy tools are useful if you work with the interactive | ||
| PhysiCell Studio Galaxy tool. | ||
| + https://usegalaxy.eu/?tool_id=interactive_tool_pcstudio&version=latest | ||
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| You will have to unzip the PhysiCell output folder before you can run | ||
| pcdl Galaxy tools on it. | ||
| + https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Funzip%2Funzip%2F6.0%2Bgalaxy0&version=latest | ||
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| More information about PhysiCell, PhysiCell Studio, and PhysiCell Data Loader | ||
| can be found here: | ||
| + https://physicell.org/index.html | ||
| + https://physicell-studio.readthedocs.io/en/latest/index.html | ||
| + https://github.com/elmbeech/physicelldataloader | ||
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| Date: 2025-06-06 | ||
| License: BSD-3-Clause | ||
| Author: Elmar Bucher |
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| <tool id="pcdl_get_anndata" name="pcdl_get_anndata" version="3.0.1+galaxy0" profile="21.05"> | ||
| <requirements> | ||
| <requirement type="package" version="3.3.7">pcdl</requirement> | ||
| </requirements> | ||
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| <stdio> <exit_code range=":" level="log" description="hello world!"/> </stdio> | ||
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There was a problem hiding this comment. hello world is not a good description :) There was a problem hiding this comment. hi @bgruening , unfortunately, this line cannot be removed. would this be acceptable? There was a problem hiding this comment. I think what you are looking for is https://docs.galaxyproject.org/en/latest/dev/schema.html#error-detection e.g. There was a problem hiding this comment. No, exactly not. There was a problem hiding this comment. Ok, that mean that your tool is reporting an error code of 1, is that the case? For any other tool, text on stderr is not a problem, you can instruct Galaxy to only react on error codes, not text on stderr. There was a problem hiding this comment. no it is not reporting an error code of 1. There was a problem hiding this comment. i followed this instruction in the galaxy documentation: |
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| <command><![CDATA[ | ||
| #import re | ||
| mkdir output_pc && | ||
| #for $file in $path: | ||
| #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier)) | ||
| ln -s '$file' output_pc/$filename && | ||
| #end for | ||
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| pcdl_get_anndata 'output_pc' $focus | ||
| --custom_data_type $custom_data_type | ||
| --microenv $microenv | ||
| --graph $graph | ||
| --physiboss $physiboss | ||
| --settingxml '$settingxml' | ||
| --verbose $verbose | ||
| --drop $drop | ||
| --keep $keep | ||
| --scale maxabs | ||
| --collapse $collapse | ||
| ]]></command> | ||
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| <inputs> | ||
| <section name="positional_arguments" title="positional arguments:" expanded="true"> | ||
| <param | ||
| name="path" label="data_collection" | ||
| type="data_collection" collection_type="list" | ||
| help="PhysiCell output data collection." | ||
| /> | ||
| <param | ||
| name="focus" label="values" | ||
| type="integer" value="1" optional="false" | ||
| help="minimal number of values a variable has to have in any of the mcds time steps to be outputted. variables that have only 1 state carry no information. None is a state too. default is 1." | ||
| /> | ||
| </section> | ||
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| <section name="options" title="options:" expanded="true"> | ||
| <param | ||
| name="custom_data_type" label="custom_data_type" | ||
| type="text" value="" optional="true" | ||
| help="parameter to specify custom_data variable types other than float (namely: int, bool, str) like this var:dtype myint:int mybool:bool mystr:str. downstream float and int will be handled as numeric, bool as Boolean, and str as categorical data. default is an empty string." | ||
| /> | ||
| <param | ||
| name="microenv" label="microenv" | ||
| type="boolean" truevalue="true" falsevalue="false" checked="true" | ||
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| help="should the microenvironment be extracted and loaded into the anndata object? setting microenv to False will use less memory and speed up processing, similar to the original pyMCDS_cells.py script. default is True." | ||
| /> | ||
| <param | ||
| name="graph" label="graph" | ||
| type="boolean" truevalue="true" falsevalue="false" checked="true" | ||
| help="should neighbor graph, attach graph, and attached spring graph be extracted and loaded into the anndata object? default is True." | ||
| /> | ||
| <param | ||
| name="physiboss" label="physiboss" | ||
| type="boolean" truevalue="true" falsevalue="false" checked="true" | ||
| help="if found, should physiboss state data be extracted and loaded into the anndata object? default is True." | ||
| /> | ||
| <param | ||
| name="settingxml" label="settingxml" | ||
| type="text" value="PhysiCell_settings.xml" optional="true" | ||
| help="the settings.xml that is loaded, from which the cell type ID label mapping, is extracted, if this information is not found in the output xml file. set to None or False if the xml file is missing! default is PhysiCell_settings.xml." | ||
| /> | ||
| <param | ||
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There was a problem hiding this comment. The verbose parameter is a bit useless in the Galaxy context. You can set it to true without exposing this parameter to the user. There was a problem hiding this comment. if possible, i would like to have it there for the user.
There was a problem hiding this comment. Yes, we do capture the verbose output, that why I think just enable it by default if it contains useful information. This way all user have all informations. And then the need for this param in the UI is not needed anymore. There was a problem hiding this comment. yes, but this might be a lot of output and uses up space that is not needed. |
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| name="verbose" label="verbose" | ||
| type="boolean" truevalue="true" falsevalue="false" checked="false" | ||
| help="setting verbose to True for more text output, while processing. default is False." | ||
| /> | ||
| <param | ||
| name="drop" label="drop" | ||
| type="text" value="" optional="true" | ||
| help="set of column labels to be dropped for the dataframe. don't worry: essential columns like ID, coordinates and time will never be dropped. Attention: when the keep parameter is given, then the drop parameter has to be an empty string! default is an empty string." | ||
| /> | ||
| <param | ||
| name="keep" label="keep" | ||
| type="text" value="" optional="true" | ||
| help="set of column labels to be kept in the dataframe. set values=1 to be sure that all variables are kept. don't worry: essential columns like ID, coordinates and time will always be kept. default is an empty string." | ||
| /> | ||
| <param | ||
| name="scale" label="scale" | ||
| type="select" display="radio" | ||
| help="specify how the data should be scaled. possible values are None, maxabs, minmax, std. None: no scaling. set scale to None if you would like to have raw data or entirely scale, transform, and normalize the data later. maxabs: maximum absolute value distance scaler will linearly map all values into a [-1, 1] interval. if the original data has no negative values, the result will be the same as with the minmax scaler (except with attributes with only one value). if the attribute has only zeros, the value will be set to 0. minmax: minimum maximum distance scaler will map all values linearly into a [0, 1] interval. if the attribute has only one value, the value will be set to 0. std: standard deviation scaler will result in sigmas. each attribute will be mean centered around 0. ddof delta degree of freedom is set to 1 because it is assumed that the values are samples out of the population and not the entire population. it is incomprehensible to me that the equivalent sklearn method has ddof set to 0. if the attribute has only one value, the value will be set to 0. default is maxabs." | ||
| > | ||
| <option value="none">none</option> | ||
| <option value="maxabs" selected="true">maxabs</option> | ||
| <option value="minmax">minmax</option> | ||
| <option value="std">std</option> | ||
| </param> | ||
| <param | ||
| name="collapse" label="collapse" | ||
| type="boolean" truevalue="true" falsevalue="false" checked="true" | ||
| help="should all mcds time steps from the time series be collapsed into one big anndata h5ad file, or a many h5ad, one h5ad for each time step?, default is True." | ||
| /> | ||
| </section> | ||
| </inputs> | ||
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| <outputs> | ||
| <collection name="anndata_h5ad" type="list"> | ||
| <discover_datasets pattern="(?P<designation>.+)\.h5ad" format="h5ad" directory="output_pc" visible="false" /> | ||
| </collection> | ||
| </outputs> | ||
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| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <section name="positional_arguments"> | ||
| <param name="path" > | ||
| <collection type="list"> | ||
| <element name="initial_attached_cells_graph.txt" value="initial_attached_cells_graph.txt" /> | ||
| <element name="initial_cell_neighbor_graph.txt" value="initial_cell_neighbor_graph.txt" /> | ||
| <element name="initial_cells.mat" value="initial_cells.mat" /> | ||
| <element name="initial_mesh0.mat" value="initial_mesh0.mat" /> | ||
| <element name="initial_microenvironment0.mat" value="initial_microenvironment0.mat" /> | ||
| <element name="initial_spring_attached_cells_graph.txt" value="initial_spring_attached_cells_graph.txt" /> | ||
| <element name="initial.svg" value="initial.svg" /> | ||
| <element name="initial.xml" value="initial.xml" /> | ||
| <element name="legend.svg" value="legend.svg" /> | ||
| <element name="output00000000_attached_cells_graph.txt" value="output00000000_attached_cells_graph.txt" /> | ||
| <element name="output00000000_cell_neighbor_graph.txt" value="output00000000_cell_neighbor_graph.txt" /> | ||
| <element name="output00000000_cells.mat" value="output00000000_cells.mat" /> | ||
| <element name="output00000000_microenvironment0.mat" value="output00000000_microenvironment0.mat" /> | ||
| <element name="output00000000_spring_attached_cells_graph.txt" value="output00000000_spring_attached_cells_graph.txt" /> | ||
| <element name="output00000000.xml" value="output00000000.xml" /> | ||
| <element name="output00000001_attached_cells_graph.txt" value="output00000001_attached_cells_graph.txt" /> | ||
| <element name="output00000001_cell_neighbor_graph.txt" value="output00000001_cell_neighbor_graph.txt" /> | ||
| <element name="output00000001_cells.mat" value="output00000001_cells.mat" /> | ||
| <element name="output00000001_microenvironment0.mat" value="output00000001_microenvironment0.mat" /> | ||
| <element name="output00000001_spring_attached_cells_graph.txt" value="output00000001_spring_attached_cells_graph.txt" /> | ||
| <element name="output00000001.xml" value="output00000001.xml" /> | ||
| <element name="final_attached_cells_graph.txt" value="final_attached_cells_graph.txt" /> | ||
| <element name="final_cell_neighbor_graph.txt" value="final_cell_neighbor_graph.txt" /> | ||
| <element name="final_cells.mat" value="final_cells.mat" /> | ||
| <element name="final_microenvironment0.mat" value="final_microenvironment0.mat" /> | ||
| <element name="final_spring_attached_cells_graph.txt" value="final_spring_attached_cells_graph.txt" /> | ||
| <element name="final.svg" value="final.svg" /> | ||
| <element name="final.xml" value="final.xml" /> | ||
| <element name="PhysiCell_settings.xml" value="PhysiCell_settings.xml" /> | ||
| </collection> | ||
| </param> | ||
| </section> | ||
| <section name="options"> | ||
| <param name="verbose" value="true" /> | ||
| <param name="collapse" value="true" /> | ||
| </section> | ||
| <output_collection name="anndata_h5ad" count="1"> | ||
| <element name="timeseries_cell_maxabs" file="timeseries_cell_maxabs.h5ad" ftype="h5ad" /> | ||
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There was a problem hiding this comment. we do have some specific asserts that you can use for hdf5 files, I guess this makes your testing more reliable https://docs.galaxyproject.org/en/latest/dev/schema.html#has-h5-attribute There was a problem hiding this comment. thank you for the link! i will look into it. |
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| </output_collection> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <section name="positional_arguments"> | ||
| <param name="path" > | ||
| <collection type="list"> | ||
| <element name="initial_attached_cells_graph.txt" value="initial_attached_cells_graph.txt" /> | ||
| <element name="initial_cell_neighbor_graph.txt" value="initial_cell_neighbor_graph.txt" /> | ||
| <element name="initial_cells.mat" value="initial_cells.mat" /> | ||
| <element name="initial_mesh0.mat" value="initial_mesh0.mat" /> | ||
| <element name="initial_microenvironment0.mat" value="initial_microenvironment0.mat" /> | ||
| <element name="initial_spring_attached_cells_graph.txt" value="initial_spring_attached_cells_graph.txt" /> | ||
| <element name="initial.svg" value="initial.svg" /> | ||
| <element name="initial.xml" value="initial.xml" /> | ||
| <element name="legend.svg" value="legend.svg" /> | ||
| <element name="output00000000_attached_cells_graph.txt" value="output00000000_attached_cells_graph.txt" /> | ||
| <element name="output00000000_cell_neighbor_graph.txt" value="output00000000_cell_neighbor_graph.txt" /> | ||
| <element name="output00000000_cells.mat" value="output00000000_cells.mat" /> | ||
| <element name="output00000000_microenvironment0.mat" value="output00000000_microenvironment0.mat" /> | ||
| <element name="output00000000_spring_attached_cells_graph.txt" value="output00000000_spring_attached_cells_graph.txt" /> | ||
| <element name="output00000000.xml" value="output00000000.xml" /> | ||
| <element name="output00000001_attached_cells_graph.txt" value="output00000001_attached_cells_graph.txt" /> | ||
| <element name="output00000001_cell_neighbor_graph.txt" value="output00000001_cell_neighbor_graph.txt" /> | ||
| <element name="output00000001_cells.mat" value="output00000001_cells.mat" /> | ||
| <element name="output00000001_microenvironment0.mat" value="output00000001_microenvironment0.mat" /> | ||
| <element name="output00000001_spring_attached_cells_graph.txt" value="output00000001_spring_attached_cells_graph.txt" /> | ||
| <element name="output00000001.xml" value="output00000001.xml" /> | ||
| <element name="final_attached_cells_graph.txt" value="final_attached_cells_graph.txt" /> | ||
| <element name="final_cell_neighbor_graph.txt" value="final_cell_neighbor_graph.txt" /> | ||
| <element name="final_cells.mat" value="final_cells.mat" /> | ||
| <element name="final_microenvironment0.mat" value="final_microenvironment0.mat" /> | ||
| <element name="final_spring_attached_cells_graph.txt" value="final_spring_attached_cells_graph.txt" /> | ||
| <element name="final.svg" value="final.svg" /> | ||
| <element name="final.xml" value="final.xml" /> | ||
| <element name="PhysiCell_settings.xml" value="PhysiCell_settings.xml" /> | ||
| </collection> | ||
| </param> | ||
| </section> | ||
| <section name="options"> | ||
| <param name="verbose" value="false" /> | ||
| <param name="collapse" value="false" /> | ||
| </section> | ||
| <output_collection name="anndata_h5ad" count="2"> | ||
| <element name="output00000000_cell_maxabs" file="output00000000_cell_maxabs.h5ad" ftype="h5ad" /> | ||
| <element name="output00000001_cell_maxabs" file="output00000000_cell_maxabs.h5ad" ftype="h5ad" /> | ||
| </output_collection> | ||
| </test> | ||
| </tests> | ||
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| <help><![CDATA[ | ||
| function to transform mcds time steps into one or many anndata objects for downstream analysis. | ||
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| homepage: https://github.com/elmbeech/physicelldataloader | ||
| ]]></help> | ||
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| <citations> | ||
| <citation type="bibtex"> | ||
| @misc{githubphysicelldataloader, | ||
| author = {Bucher, Elmar}, | ||
| year = {2025}, | ||
| title = {physicelldataloader}, | ||
| publisher = {GitHub}, | ||
| journal = {GitHub repository}, | ||
| url = {https://github.com/elmbeech/physicelldataloader}, | ||
| }</citation> | ||
| </citations> | ||
| </tool> | ||
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