Mercurial > repos > ebi-gxa > scmap_index_cluster
view scmap_index_cluster.xml @ 1:e6d99b0652ec draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
author | ebi-gxa |
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date | Fri, 25 Oct 2019 08:45:05 -0400 |
parents | 6b24ebf5b7fb |
children | 63f1a27dce34 |
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<tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> <description>calculates centroids of each cell type and merges them into a single table</description> <macros> <import>scmap_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "preprocessed_${input_single_cell_experiment}" && scmap-index-cluster.R --input-object-file "preprocessed_${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' ]]></command> <inputs> <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" /> <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." /> </inputs> <outputs> <data name="output_single_cell_experiment" format="rdata" /> <data name="plot" format="png" /> </outputs> <tests> <test> <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> <output name="output_single_cell_experiment" file="index_cluster.rds"/> <output name="plot" file="index_cluster.png"/> </test> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>