Mercurial > repos > ebi-gxa > scpred_traint_test_split
diff scpred_train_test_split.xml @ 0:8ec19f24fcf3 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
author | ebi-gxa |
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date | Wed, 08 Apr 2020 06:37:16 -0400 |
parents | |
children | a6d66c9953ed |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scpred_train_test_split.xml Wed Apr 08 06:37:16 2020 -0400 @@ -0,0 +1,37 @@ +<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>CPM normalise and partition into train/test data</description> + <macros> + <import>scpred_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command> + <inputs> + <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" /> + <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" /> + <param type="text" name="cell_types_col" label="Column name for assigned cell types" /> + <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" /> + </inputs> + <outputs> + <data name="training_mat" format="rdata" /> + <data name="test_mat" format="rdata" /> + <data name="training_labs" format="txt" /> + <data name="test_labs" format="txt" /> + </outputs> + <tests> + <test> + <param name="input_sce_object" value="pollen_cpm.rds" /> + <param name="cell_types_col" value="cell_type2" /> + <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/> + <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/> + <output name="training_labs" file="train_metadata.txt" compare="sim_size" /> + <output name="test_labs" file="test_metadata.txt" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool>