Mercurial > repos > ebi-gxa > scpred_predict_labels

comparison scpred_predict.xml @ 0:c54f0e1a3bd8 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
author ebi-gxa
date Wed, 08 Apr 2020 06:18:58 -0400
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children 051f5801c819
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-1:000000000000 0:c54f0e1a3bd8
1 <tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy0">
2 <description>Make cell type predictions using trained model.</description>
3 <macros>
4 <import>scpred_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --test-labels "${test_labels}" --cell-types-column "${cell_types_column}" --output-path "${output_tbl_path}" --plot-path "${plot_path}" --confusion-table "${confusion_table}"
9 ]]></command>
10 <inputs>
11 <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
12 <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
13 <param type="data" name="test_labels" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />
14 <param type="text" name="cell_types_column" value="cell_type2" label="Cell types column name" help="Column name of true labels in provided metadata file" />
15 </inputs>
16 <outputs>
17 <data name="output_tbl_path" format="txt" />
18 <data name="plot_path" format="txt" />
19 <data name="confusion_table" format="txt" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="input_object" value="scPred_trained.rds" />
24 <param name="pred_data" value="test_matrix.mtx" />
25 <param name="test_labels" value="test_metadata.txt" />
26 <output name="output_tbl_path" file="predictions_table.txt" compare="sim_size"/>
27 </test>
28 </tests>
29 <help><![CDATA[
30 @HELP@
31
32 @VERSION_HISTORY@
33 ]]></help>
34 <expand macro="citations" />
35 </tool>