Mercurial > repos > ebi-gxa > scmap_index_cell

comparison scmap_index_cell.xml @ 8:441df83ffc7c draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 519352db368942656aa9cb994da421cddad5d746"
author ebi-gxa
date Wed, 15 Jul 2020 09:24:15 -0400
parents db43f55890d9
children 0f5e46b0981a
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7:11b4b9b85b9c 8:441df83ffc7c
1 <tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy3" 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 "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && 8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
9 scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --number-chunks '$n_chunks' --number-clusters '$n_clusters' --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'
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 $n_chunks
14 --number-chunks '$n_chunks'
15 #end if
16 #if $n_clusters
17 --number-clusters '$n_clusters'
18 #end if
19
13 ]]></command> 20 ]]></command>
14 <inputs> 21 <inputs>
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'" /> 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'" />
16 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" /> 23 <param name="n_chunks" type="integer" label="Number of chunks" optional="true" help="Number of chunks into which the expr matrix is split" />
17 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" /> 24 <param name="n_clusters" type="integer" label="Number of clusters" optional="true" help="Number of clusters per group for k-means clustering" />
18 <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" />
19 <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." /> 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." />
20 </inputs> 27 </inputs>
21 <outputs> 28 <outputs>
22 <data name="output_single_cell_experiment" format="rdata" /> 29 <data name="output_single_cell_experiment" format="rdata" />
23 </outputs> 30 </outputs>
24 <tests> 31 <tests>
25 <test> 32 <test>
26 <param name="n_chunks" value="50" />
27 <param name="n_clusters" value="9" />
28 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/> 33 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
29 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/> 34 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
30 </test> 35 </test>
31 </tests> 36 </tests>
32 <help><![CDATA[ 37 <help><![CDATA[