Mercurial > repos > ebi-gxa > scmap_index_cluster

comparison scmap_index_cluster.xml @ 3:9b60d5972dbd draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:25:27 -0400
parents 63f1a27dce34
children b65f8ef6ca30
comparison
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2:63f1a27dce34 3:9b60d5972dbd
3 <macros> 3 <macros>
4 <import>scmap_macros.xml</import> 4 <import>scmap_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cluster.R --input-object-file "${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
9 #if $train_id
10 --train-id '${train_id}'
11 #end if
9 ]]></command> 12 ]]></command>
10 <inputs> 13 <inputs>
11 <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'" /> 14 <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'" />
15 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
12 <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." /> 16 <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." />
13 </inputs> 17 </inputs>
14 <outputs> 18 <outputs>
15 <data name="output_single_cell_experiment" format="rdata" /> 19 <data name="output_single_cell_experiment" format="rdata" />
16 <data name="plot" format="png" /> 20 <data name="plot" format="png" />