Mercurial > repos > ebi-gxa > seurat_run_tsne
changeset 2:fd0fc93b3c87 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
| author | ebi-gxa |
|---|---|
| date | Fri, 10 Jul 2020 21:52:46 -0400 |
| parents | 13a27436f8ee |
| children | 050fe6894b74 |
| files | seurat_macros.xml seurat_run_tsne.xml |
| diffstat | 2 files changed, 9 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/seurat_macros.xml Mon Nov 25 06:11:40 2019 -0500 +++ b/seurat_macros.xml Fri Jul 10 21:52:46 2020 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0.0.6</token> + <token name="@VERSION@">0.0.7</token> <token name="@SEURAT_VERSION@">3.1.1</token> <xml name="requirements"> <requirements> @@ -97,6 +97,8 @@ <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +3.1.1_0.0.7: Exposes perplexity and enables tab input. + 3.1.1_0.0.6+galaxy0: Moved to Seurat 3. Find clusters: removed dims-use, k-param, prune-snn. @@ -121,6 +123,7 @@ url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, } </citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </xml> </macros>
--- a/seurat_run_tsne.xml Mon Nov 25 06:11:40 2019 -0500 +++ b/seurat_run_tsne.xml Fri Jul 10 21:52:46 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> +<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@+galaxy1"> <description>run t-SNE dimensionality reduction</description> <macros> <import>seurat_macros.xml</import> @@ -31,6 +31,9 @@ #if $adv.random_seed --random-seed '$adv.random_seed' #end if +#if $adv.perplexity + --perplexity '$adv.perplexity' +#end if @OUTPUT_OBJECT@ --output-embeddings-file output_embed @@ -51,6 +54,7 @@ <option value="2" selected="true">2</option> <option value="3">3</option> </param> + <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/> <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/> </section> </inputs>