Mercurial > repos > ebi-gxa > scmap_index_cell

comparison scmap_index_cell.xml @ 11:dd0b44bd359a 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 13:43:08 +0000
parents 7c3f9606ed0a
children
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10:7c3f9606ed0a 11:dd0b44bd359a
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 "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
9 scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' 9 scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' --remove-mat '${remove_mat}'
10 #if $train_id 10 #if $train_id
11 --train-id '${train_id}' 11 --train-id '${train_id}'
12 #end if 12 #end if
13 #if $n_chunks 13 #if $n_chunks
14 --number-chunks '$n_chunks' 14 --number-chunks '$n_chunks'
21 <inputs> 21 <inputs>
22 <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'" /> 22 <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'" />
23 <param name="n_chunks" type="integer" label="Number of chunks" optional="true" value="0" help="Number of chunks into which the expr matrix is split" /> 23 <param name="n_chunks" type="integer" label="Number of chunks" optional="true" value="0" help="Number of chunks into which the expr matrix is split" />
24 <param name="n_clusters" type="integer" label="Number of clusters" optional="true" value="0" help="Number of clusters per group for k-means clustering" /> 24 <param name="n_clusters" type="integer" label="Number of clusters" optional="true" value="0" help="Number of clusters per group for k-means clustering" />
25 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" /> 25 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
26 <param type="boolean" name="remove_mat" checked="false" label="Remove Matrix" help="Should the expression data be removed after classifier is trained?" />
26 <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." /> 27 <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
27 </inputs> 28 </inputs>
28 <outputs> 29 <outputs>
29 <data name="output_single_cell_experiment" format="rdata" /> 30 <data name="output_single_cell_experiment" format="rdata" />
30 </outputs> 31 </outputs>
31 <tests> 32 <tests>
32 <test> 33 <test>
33 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> 34 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
34 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/> 35 <param name="remove_mat" value="true" />
36 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size" delta="10000000"/>
35 </test> 37 </test>
36 </tests> 38 </tests>
37 <help><![CDATA[ 39 <help><![CDATA[
38 @HELP@ 40 @HELP@
39 41