Mercurial > repos > ebi-gxa > seurat_run_tsne
diff seurat_run_tsne.xml @ 1:13a27436f8ee draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author | ebi-gxa |
---|---|
date | Mon, 25 Nov 2019 06:11:40 -0500 |
parents | 3aea769deab1 |
children | fd0fc93b3c87 |
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--- a/seurat_run_tsne.xml Wed Apr 03 11:19:13 2019 -0400 +++ b/seurat_run_tsne.xml Mon Nov 25 06:11:40 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1"> +<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> <description>run t-SNE dimensionality reduction</description> <macros> <import>seurat_macros.xml</import> @@ -8,8 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ seurat-run-tsne.R ---input-object-file '$input' - +@INPUT_OBJECT@ #if $genes_use: --genes-use '$genes_use' #end if @@ -23,29 +22,48 @@ #if not $adv.do_fast: --do-fast '$adv.do_fast' #end if +#if $adv.tsne_method + --tsne-method '$adv.tsne_method' +#end if +#if $adv.dim_embed + --dim_embed '$adv.dim_embed' +#end if +#if $adv.random_seed + --random-seed '$adv.random_seed' +#end if ---output-object-file '$output' +@OUTPUT_OBJECT@ --output-embeddings-file output_embed ]]></command> <inputs> - <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> <expand macro="genes-use-input"/> <section name="adv" title="Advanced Options"> <expand macro="dims-use-input"/> <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/> + <param label="tSNE method" optional="true" name="tsne_method" argument="--tsne-method" type="select" help="Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE"> + <option value="Rtsne" selected="true">Rtsne</option> + <option value="Flt-SNE">Flt-SNE</option> + </param> + <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE"> + <option value="2" selected="true">2</option> + <option value="3">3</option> + </param> + <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/> </section> </inputs> <outputs> - <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> + <expand macro="output_files"/> <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> </outputs> <tests> <test> <param name="input" ftype="rdata" value="out_findclust.rds"/> - <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> + <output name="rds_seurat_file" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -58,10 +76,9 @@ interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. -Run t-SNE dimensionality reduction on selected features. Has the option of -running in a reduced dimensional space (i.e. spectral tSNE, recommended), -or running based on a set of genes. For details about stored TSNE calculation -parameters, see standard output of the tool. +Run t-SNE dimensionality reduction on selected features. Has the option of running +in a reduced dimensional space (i.e. spectral tSNE, recommended), or +running based on a set of genes. -----