Mercurial > repos > ebi-gxa > scmap_index_cell

comparison scmap_index_cell.xml @ 2:dd2a84734b87 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
author ebi-gxa
date Fri, 03 Apr 2020 06:36:06 -0400
parents 17b3d7e04b3c
children 5593b0744de9
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1:17b3d7e04b3c 2:dd2a84734b87
1 <tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> 1 <tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description> 2 <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</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-cell.R --input-object-file "preprocessed_${input_single_cell_experiment}" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
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="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" /> 12 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
13 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" /> 13 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
19 <tests> 19 <tests>
20 <test> 20 <test>
21 <param name="n_chunks" value="50" /> 21 <param name="n_chunks" value="50" />
22 <param name="n_clusters" value="9" /> 22 <param name="n_clusters" value="9" />
23 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> 23 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
24 <output name="output_single_cell_experiment" file="index_cell.rds"/> 24 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
25 </test> 25 </test>
26 </tests> 26 </tests>
27 <help><![CDATA[ 27 <help><![CDATA[
28 @HELP@ 28 @HELP@
29 29