| Next changeset 1:dcfcad35e847 (2022-08-29) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5 |
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added:
main_macros.xml mcmicro_to_anndata.py scimap_phenotyping.py scimap_phenotyping.xml scimap_spatial.py test-data/imc.h5ad test-data/manual_gates.csv test-data/mcmicro_output.csv test-data/phenotype_workflow.csv test-data/tutorial_data.h5ad test-data/tutorial_data_pheno.h5ad |
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| diff -r 000000000000 -r 7ed4b55b11f7 main_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/main_macros.xml Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <token name="@TOOL_VERSION@">0.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + + <xml name="scimap_requirements"> + <requirements> + <container type="docker">quay.io/goeckslab/scimap:0.17.7</container> + <yield /> + </requirements> + </xml> + + <xml name="macro_stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + </xml> + + <xml name="scimap_spatial_options" token_label="spatial_aggregate"> + <section name="options" title="Advanced Options" expanded="false"> + <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Column name containing the x-coordinates values" /> + <param argument="y_coordinate" type="text" value="Y_centroid" optional="false" label="Column name containing the y-coordinates values" /> + <yield/> + <param argument="imageid" type="text" value="imageid" optional="true" label="Column name of the column containing the image id" /> + <param argument="subset" type="text" value="" optional="true" label="Imageid of a single image to be subsetted for analyis" /> + <param argument="label" type="text" value="@LABEL@" optional="true" label="Key for the returned data" help="Stored in adata.obs" /> + </section> + </xml> +</macros> |
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| diff -r 000000000000 -r 7ed4b55b11f7 mcmicro_to_anndata.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mcmicro_to_anndata.py Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,45 @@ +import argparse +import json +import warnings + +import scimap as sm + + +def main(inputs, outfile): + """ + Parameter + --------- + inputs : str + File path to galaxy tool parameter. + + outfile : str + File path to estimator. + """ + warnings.simplefilter('ignore') + + with open(inputs, 'r') as param_handler: + params = json.load(param_handler) + + image_path = params['image_path'] + drop_markers = params['drop_markers'] + if not drop_markers: + drop_markers = None + else: + drop_markers = [x.strip() for x in drop_markers.split(',')] + options = params['options'] + for k, v in options.items(): + if v == '': + options[k] = None + + adata = sm.pp.mcmicro_to_scimap(image_path, drop_markers=drop_markers, **options) + + adata.write(outfile) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-i", "--inputs", dest="inputs", required=True) + aparser.add_argument("-e", "--outfile", dest="outfile", required=True) + args = aparser.parse_args() + + main(args.inputs, args.outfile) |
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| diff -r 000000000000 -r 7ed4b55b11f7 scimap_phenotyping.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scimap_phenotyping.py Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,73 @@ +import argparse +import warnings + +import pandas as pd +import scimap as sm +from anndata import read_h5ad + + +def main( + adata, + output, + gating_workflow, + gating_workflow_ext, + manual_gates=None, + manual_gates_ext=None, + rescale_plots=False +): + """ + Parameter + --------- + adata : str + File path to the input AnnData. + output : str + File path to the output AnnData. + gating_workflow : str + File path to the gating workflow. + gating_workflow_ext : str + Datatype for gating workflow, either 'csv' or 'tabular'. + manual_gates : str + File path to the munual gating. + manual_gates_ext : str + Datatype for munual gate, either 'csv' or 'tabular'. + rescale_plots : boolean + Save plots from rescaling. + """ + warnings.simplefilter('ignore') + + adata = read_h5ad(adata) + # Rescale data + if manual_gates: + sep = ',' if manual_gates_ext == 'csv' else '\t' + manual_gates = pd.read_csv(manual_gates, sep=sep) + + adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots) + + # Phenotype cells + # Load the gating workflow + sep = ',' if gating_workflow_ext == 'csv' else '\t' + phenotype = pd.read_csv(gating_workflow, sep=sep) + adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype") + + # Summary of the phenotyping + print(adata.obs['phenotype'].value_counts()) + + adata.write(output) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-a", "--adata", dest="adata", required=True) + aparser.add_argument("-o", "--output", dest="output", required=True) + aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True) + aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True) + aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False) + aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False) + aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true", + default=False, required=False) + + args = aparser.parse_args() + + main(args.adata, args.output, args.gating_workflow, + args.gating_workflow_ext, args.manual_gates, + args.manual_gates_ext, args.rescale_plots) |
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| diff -r 000000000000 -r 7ed4b55b11f7 scimap_phenotyping.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scimap_phenotyping.xml Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,75 @@ +<tool id="scimap_phenotyping" name="Single Cell Phenotyping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>using scimap</description> + <macros> + <import>main_macros.xml</import> + </macros> + + <expand macro="scimap_requirements"/> + <expand macro="macro_stdio" /> + <version_command>echo "@VERSION@"</version_command> + <command> + <![CDATA[ + python '$__tool_directory__/scimap_phenotyping.py' + --adata '$anndata' + #if $manual_gates + --manual_gates '$manual_gates' + --manual_gates_ext '${manual_gates.ext}' + #end if + --gating_workflow '$gating_workflow' + --gating_workflow_ext '${gating_workflow.ext}' + #if $rescale_plots + --rescale_plots + #end if + --output '$output' + + ]]> + </command> + <configfiles> + <inputs name="inputs" /> + </configfiles> + <inputs> + <param name="anndata" type="data" format="h5ad" label="Select the input anndata" /> + <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating + based on gaussian mixture modeling will be executed. Optional."/> + <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" /> + <param name="rescale_plots" type="boolean" checked="false" label="Save the GMM gates plots If True"/> + </inputs> + <outputs> + <data format="h5ad" name="output" /> + <collection name="gmm_plots" type="list" label="${tool.name}: GMM-plots"> + <filter>rescale_plots</filter> + <discover_datasets pattern="__designation_and_ext__" directory="auto_gating" ext="png"/> + </collection> + </outputs> + <tests> + <test> + <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" /> + <param name="manual_gates" value="manual_gates.csv" ftype="csv" /> + <param name="gating_workflow" value="phenotype_workflow.csv" ftype="csv" /> + <output name="output"> + <assert_contents> + <has_h5_keys keys="obs/phenotype" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ +**What it does** + +This tool generates single cell phenotyping using either manual gating or auto gating (gaussian mixture modeling) implemented in Scimap. + +**Input** + +AnnData. + +**Output** + +Anndata with "obs/phenotype" added. + + + ]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 7ed4b55b11f7 scimap_spatial.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scimap_spatial.py Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,59 @@ +import argparse +import json +import warnings + +import scimap as sm +from anndata import read_h5ad + + +def main(inputs, anndata, output): + """ + Parameter + --------- + inputs : str + File path to galaxy tool parameter. + anndata : str + File path to anndata containing phenotyping info. + output : str + File path to output. + """ + warnings.simplefilter('ignore') + + with open(inputs, 'r') as param_handler: + params = json.load(param_handler) + + adata = read_h5ad(anndata) + + tool = params['analyses']['selected_tool'] + tool_func = getattr(sm.tl, tool) + + options = params['analyses']['options'] + if tool == 'cluster': + options['method'] = params['analyses']['method'] + subset_genes = options.pop('subset_genes') + if subset_genes: + options['subset_genes'] = \ + [x.strip() for x in subset_genes.split(',')] + sub_cluster_group = options.pop('sub_cluster_group') + if sub_cluster_group: + options['sub_cluster_group'] = \ + [x.strip() for x in sub_cluster_group.split(',')] + + for k, v in options.items(): + if v == '': + options[k] = None + + tool_func(adata, **options) + + adata.write(output) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-i", "--inputs", dest="inputs", required=True) + aparser.add_argument("-e", "--output", dest="output", required=True) + aparser.add_argument("-a", "--anndata", dest="anndata", required=True) + + args = aparser.parse_args() + + main(args.inputs, args.anndata, args.output) |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/imc.h5ad |
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| Binary file test-data/imc.h5ad has changed |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/manual_gates.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/manual_gates.csv Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,19 @@ +markers,gate +ASMA,6.6 +CD163,6.6 +CD206,7.5 +CD68,6.2 +CD20,7.8 +CD21,8 +CD3D,6.5 +CD45,7.3 +CD56,8.7 +CD8A,6.5 +FOXP3,5.2 +CD11B,6.7 +CD11C,6.3 +CD15,7.9 +CD4,7.4 +PD1,7.9 +HLADR,6.7 +CD25,7 \ No newline at end of file |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/mcmicro_output.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcmicro_output.csv Tue Jul 19 20:29:22 2022 +0000 |
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| b'@@ -0,0 +1,4826 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No newline at end of file\n' |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/phenotype_workflow.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotype_workflow.csv Tue Jul 19 20:29:22 2022 +0000 |
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| @@ -0,0 +1,23 @@ +,,ASMA,CD163,CD206,CD68,CD20,CD21,CD3D,CD45,CD56,CD8A,FOXP3,CD11B,CD11C,CD15,CD4,PD1,HLADR,CD25 +all,Other Immune cells,,,,,,,,pos,,,,,,,,,, +all,ASMA+ cells,pos,,,,,,,,,,,,,,,,, +Other Immune cells,T cells,,,,,,,pos,,,,,,,,,,, +Other Immune cells,B cells,,,,,pos,,,,,,,,,,,,, +Other Immune cells,Myeloid Lineage,,anypos,anypos,anypos,,,,,,,,anypos,anypos,,,,, +Other Immune cells,NK cells,,,,,,,,,pos,,,,,,,,, +Other Immune cells,Granulocytes,,,,,,,,,,,,,,pos,,,, +Myeloid Lineage,T cells,,,,,,,pos,,,,,,,,,,, +Myeloid Lineage,B cells,,,,,pos,,,,,,,,,,,,, +Myeloid Lineage,NK cells,,,,,,,,,pos,,,,,,,,, +Myeloid Lineage,Granulocytes,,,,,,,,,,,,,,pos,,,, +T cells,CD4 T cells,,,,,,,,,,,,,,,pos,,, +T cells,CD8 T cells,,,,,,,,,,pos,,,,,,,, +CD4 T cells,Regulatory T cells,,,,,,,,,,,pos,,,,,,, +CD4 T cells,Follicular Helper T cells,,,,,,,,,,,,,,,,pos,, +CD8 T cells,PD1+ T cells,,,,,,,,,,,,,,,,pos,, +Myeloid Lineage,CD68+ Macrophages,,,,pos,,,,,,,,,,,,,, +Myeloid Lineage,M2 Macrophages,,anypos,anypos,,,,,,,,,,,,,,, +Myeloid Lineage,Myeloid Dendritic cells,,,,,,,,,,,,,,,,,pos, +Myeloid Lineage,Follicular Dendritic cells,,,,,,pos,,,,,,,,,,,, +CD68+ Macrophages,M1 Macrophages,,,,,,,,,,,,,,,,,pos, +Myeloid Dendritic cells,CD25+ Dendritic cells,,,,,,,,,,,,,,,,,,pos \ No newline at end of file |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/tutorial_data.h5ad |
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| diff -r 000000000000 -r 7ed4b55b11f7 test-data/tutorial_data_pheno.h5ad |
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