Mercurial > repos > ebi-gxa > scmap_index_cluster
comparison scmap_index_cluster.xml @ 2:63f1a27dce34 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
author | ebi-gxa |
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date | Fri, 03 Apr 2020 06:35:36 -0400 |
parents | e6d99b0652ec |
children | 9b60d5972dbd |
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1:e6d99b0652ec | 2:63f1a27dce34 |
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1 <tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> | 1 <tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
2 <description>calculates centroids of each cell type and merges them into a single table</description> | 2 <description>calculates centroids of each cell type and merges them into a single table</description> |
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 "${input_single_cell_experiment}" --output-sce-object "preprocessed_${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' | 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' |
9 ]]></command> | 9 ]]></command> |
10 <inputs> | 10 <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'" /> | 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'" /> |
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." /> | 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." /> |
13 </inputs> | 13 </inputs> |
16 <data name="plot" format="png" /> | 16 <data name="plot" format="png" /> |
17 </outputs> | 17 </outputs> |
18 <tests> | 18 <tests> |
19 <test> | 19 <test> |
20 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> | 20 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> |
21 <output name="output_single_cell_experiment" file="index_cluster.rds"/> | 21 <output name="output_single_cell_experiment" file="index_cluster.rds" compare="sim_size"/> |
22 <output name="plot" file="index_cluster.png"/> | 22 <output name="plot" file="index_cluster.png"/> |
23 </test> | 23 </test> |
24 </tests> | 24 </tests> |
25 <help><![CDATA[ | 25 <help><![CDATA[ |
26 @HELP@ | 26 @HELP@ |