Mercurial > repos > ebi-gxa > scmap_index_cluster

comparison scmap_index_cluster.xml @ 0:6b24ebf5b7fb draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author ebi-gxa
date Mon, 16 Sep 2019 09:56:06 -0400
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children e6d99b0652ec
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-1:000000000000 0:6b24ebf5b7fb
1 <tool id="scmap_index_cluster" name="scmap index clusters" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
2 <description>calculates centroids of each cell type and merges them into a single table</description>
3 <macros>
4 <import>scmap_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 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>
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'" />
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>
14 <outputs>
15 <data name="output_single_cell_experiment" format="rdata" />
16 <data name="plot" format="png" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
21 <output name="output_single_cell_experiment" file="index_cluster.rds"/>
22 <output name="plot" file="index_cluster.png"/>
23 </test>
24 </tests>
25 <help><![CDATA[
26 @HELP@
27
28 @VERSION_HISTORY@
29 ]]></help>
30 <expand macro="citations" />
31 </tool>