Mercurial > repos > ebi-gxa > scmap_index_cluster

comparison scmap_index_cluster.xml @ 9:4ff68faee6e1 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:43:29 +0000
parents 1949832b448c
children
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8:1949832b448c 9:4ff68faee6e1
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 "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot' 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 --remove-mat '${remove_mat}'
9 #if $train_id 10 #if $train_id
10 --train-id '${train_id}' 11 --train-id '${train_id}'
11 #end if 12 #end if
12 ]]></command> 13 ]]></command>
13 <inputs> 14 <inputs>
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="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
16 <param type="boolean" name="remove_mat" checked="false" label="Remove Matrix" help="Should the expression data be removed after classifier is trained?" />
15 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" /> 17 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
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." /> 18 <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." />
17 </inputs> 19 </inputs>
18 <outputs> 20 <outputs>
19 <data name="output_single_cell_experiment" format="rdata" /> 21 <data name="output_single_cell_experiment" format="rdata" />
20 <data name="plot" format="png" /> 22 <data name="plot" format="png" />
21 </outputs> 23 </outputs>
22 <tests> 24 <tests>
23 <test> 25 <test>
24 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> 26 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
25 <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size"/> 27 <param name="remove_mat" value="true" />
26 <output name="plot" file="index_cluster.png"/> 28 <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size" delta="1000000000"/>
29 <output name="plot" file="index_cluster.png" compare="sim_size" delta="1000000000"/>
27 </test> 30 </test>
28 </tests> 31 </tests>
29 <help><![CDATA[ 32 <help><![CDATA[
30 @HELP@ 33 @HELP@
31 34