Mercurial > repos > ebi-gxa > celltypist_predict

comparison celltypist.xml @ 1:df005630100e draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4dd95e3e6c059cc9df47f5d08e4f3f8b618830f1-dirty
author ebi-gxa
date Wed, 19 Feb 2025 12:10:17 +0000
parents a7d6985ba791
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0:a7d6985ba791 1:df005630100e
1 <tool id="celltypist_predict" name="CellTypist: Predict Cell Types" version="1.6.3+galaxy0" profile="20.05" license="MIT"> 1 <tool id="celltypist_predict" name="CellTypist: Predict Cell Types" version="1.6.3+galaxy1" profile="20.05" license="MIT">
2 <description>Predict cell types using an existing CellTypist model.</description> 2 <description>Predict cell types using an existing CellTypist model.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.3">celltypist</requirement> 4 <requirement type="package" version="1.6.3">celltypist</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
53 <param format="mtx,txt" type="data" name="data" label="Input matrix (mtx file)" help="The input data for prediction."/> 53 <param format="mtx,txt" type="data" name="data" label="Input matrix (mtx file)" help="The input data for prediction."/>
54 <param format="txt,tabular" type="data" name="gene_file" label="Gene file" help="The file containing one gene per line corresponding to the genes in the input data (required for .mtx data)."/> 54 <param format="txt,tabular" type="data" name="gene_file" label="Gene file" help="The file containing one gene per line corresponding to the genes in the input data (required for .mtx data)."/>
55 <param format="txt,tabular" type="data" name="cell_file" label="Cell file" help="The file containing one cell per line corresponding to the cells in the input data (required for .mtx data)."/> 55 <param format="txt,tabular" type="data" name="cell_file" label="Cell file" help="The file containing one cell per line corresponding to the cells in the input data (required for .mtx data)."/>
56 </when> 56 </when>
57 </conditional> 57 </conditional>
58 <param format="data" type="data" name="model_file" optional="false" label="Model file" help="The existing CellTypist model file in .pkl format."/> 58 <param format="data" type="data" name="model_file" optional="false" label="Model file" help="A CellTypist model file in .pkl format."/>
59 <param type="boolean" argument="--normalize" label="Normalize" truevalue="--normalize" falsevalue="" help="If raw counts are provided in the AnnData object, they need to be normalized."/> 59 <param type="boolean" argument="--normalize" label="Normalize" truevalue="--normalize" falsevalue="" help="If raw counts are provided in the AnnData object, they need to be normalized."/>
60 <param type="boolean" argument="--transpose_input" label="Transpose input" truevalue="--transpose_input" falsevalue="" help="If the provided matrix is in the gene-by-cell format, please transpose the input to cell-by-gene format."/> 60 <param type="boolean" argument="--transpose_input" label="Transpose input" truevalue="--transpose_input" falsevalue="" help="If the provided matrix is in the gene-by-cell format, please transpose the input to cell-by-gene format."/>
61 <param type="select" name="mode" label="Mode" help="Mode for the prediction (e.g., best match, majority vote)."> 61 <param type="select" name="mode" label="Mode" help="Mode for the prediction (e.g., best match, majority vote).">
62 <option value="best_match" selected="true">Best match</option> 62 <option value="best_match" selected="true">Best match</option>
63 <option value="prob_match">Probability match</option> 63 <option value="prob_match">Probability match</option>
65 <param type="float" name="p_thres" value="0.5" label="Probability threshold" help="Probability threshold for assigning a cell type in a multiclass problem. Ignored if Mode set to Best match."/> 65 <param type="float" name="p_thres" value="0.5" label="Probability threshold" help="Probability threshold for assigning a cell type in a multiclass problem. Ignored if Mode set to Best match."/>
66 <param type="boolean" argument="--majority_voting" label="Majority voting" truevalue="--majority_voting" falsevalue="" help="Refine the predicted labels by running the majority voting classifier after over-clustering."/> 66 <param type="boolean" argument="--majority_voting" label="Majority voting" truevalue="--majority_voting" falsevalue="" help="Refine the predicted labels by running the majority voting classifier after over-clustering."/>
67 <param type="text" name="over_clustering" label="Over-clustering" help="If majority voting is set to True, specify the type of over-clustering that is to be performed. This can be specified in the AnnData or an input file specifying the over-clustering per cell. If not present, then the default heuristic over-clustering based on input data will be used."/> 67 <param type="text" name="over_clustering" label="Over-clustering" help="If majority voting is set to True, specify the type of over-clustering that is to be performed. This can be specified in the AnnData or an input file specifying the over-clustering per cell. If not present, then the default heuristic over-clustering based on input data will be used."/>
68 </inputs> 68 </inputs>
69 <outputs> 69 <outputs>
70 <data format="csv" name="output_predictions" label="${tool.name} on ${on_string}: cell typing table"/> 70 <data format="tabular" name="output_predictions" label="${tool.name} on ${on_string}: cell typing table"/>
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test expect_num_outputs="1"> 73 <test expect_num_outputs="1">
74 <param name="model_file" value="Healthy_COVID19_PBMC.pkl"/> 74 <param name="model_file" value="Healthy_COVID19_PBMC.pkl"/>
75 <param name="normalize" value="true"/> 75 <param name="normalize" value="true"/>
82 </conditional> 82 </conditional>
83 <output name="output_predictions"> 83 <output name="output_predictions">
84 <assert_contents> 84 <assert_contents>
85 <has_text text="MAIT"/> 85 <has_text text="MAIT"/>
86 <has_n_lines n="2701"/> 86 <has_n_lines n="2701"/>
87 <!-- <has_line line=""/> -->
88 <!-- <has_line_matching expression=""/> -->
89 <has_n_columns n="2"/> 87 <has_n_columns n="2"/>
90 </assert_contents> 88 </assert_contents>
91 </output> 89 </output>
92 </test> 90 </test>
93 </tests> 91 </tests>