Mercurial > repos > ebi-gxa > seurat_find_clusters
changeset 1:bdabb6af06e4 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 06:09:15 -0500 |
| parents | 8ea738667314 |
| children | 0715bcb14547 |
| files | seurat_find_clusters.xml seurat_macros.xml |
| diffstat | 2 files changed, 130 insertions(+), 49 deletions(-) [+] |
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--- a/seurat_find_clusters.xml Wed Apr 03 11:17:04 2019 -0400 +++ b/seurat_find_clusters.xml Mon Nov 25 06:09:15 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="seurat_find_clusters" name="Seurat FindClusters" version="2.3.1+galaxy1"> +<tool id="seurat_find_clusters" name="Seurat FindClusters" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> <description>find clusters of cells</description> <macros> <import>seurat_macros.xml</import> @@ -8,30 +8,10 @@ <command detect_errors="exit_code"><![CDATA[ seurat-find-clusters.R - --input-object-file '$input' - --output-object-file '$output' + @INPUT_OBJECT@ + @OUTPUT_OBJECT@ --output-text-file output_tab - #if $genes_use: - --genes-use '$genes_use' - #end if - - #if str($adv.reduction_type): - --reduction-type '$adv.reduction_type' - #end if - - #if str($adv.dims_use): - --dims-use \$(seq -s , 1 '$adv.dims_use') - #end if - - #if str($adv.k_num_clusters): - --k-param '$adv.k_num_clusters' - #end if - - #if str($adv.prune_snn): - --prune-snn '$adv.prune_snn' - #end if - #if str($adv.resolution): --resolution '$adv.resolution' #end if @@ -40,31 +20,58 @@ --algorithm '$adv.algorithm' #end if + #if str($adv.modularity_fxn): + --modularity-fxn '$adv.modularity_fxn' + #end if + + #if str($adv.method): + --method '$adv.method' + #end if + + #if str($adv.graph_name): + --graph-name '$adv.graph_name' + #end if + + #if str($adv.nrandom_starts): + --nrandom-starts '$adv.nrandom_starts' + #end if + + $adv.group_singletons + + + ## TODO add pdf support as optional ]]></command> <inputs> - <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Seurat object produced by Seurat run PCA or other." /> - <expand macro="genes-use-input"/> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> <section name="adv" title="Advanced Options"> - <param name="reduction_type" argument="--reduction-type" optional="true" type="select" label="Dimensional reduction type" help="dimensional reduction technique to use in construction of SNN graph. (e.g. 'pca', 'ica'). PCA by default."> - <option value="pca" selected="true">PCA</option> - <option value="ica">ICA</option> - </param> - <expand macro="dims-use-input"/> - <param name="k_num_clusters" argument="--k-param" optional="true" type="integer" label="Number of clusters (k) to compute" help="Defines k for the k-nearest neighbor algorithm."/> - <param name="prune_snn" argument="--prune-snn" optional="true" type="float" label="Prune SNN cutoff" help="Sets the cutoff for acceptable Jaccard distances when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 — no pruning, 1 — prune everything). Defaults to 1/15."/> <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution" help="Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities. Defaults to 0.8."/> <param name="algorithm" argument="--algorithm" optional="true" type="select" label="Modularity organization algorithm"> <option value="1" selected="true">Louvain</option> <option value="2">Louvain algorithm with multilevel refinement</option> <option value="3">SLM algorithm</option> + <option value="4">Leiden</option> </param> + <param name="modularity_fxn" argument="--modularity-fxn" optional="true" type="select" label="Modularity function"> + <option value="1" selected="true">Standard</option> + <option value="2">Alternative</option> + </param> + <param name="method" argument="--method" type="select" label="Method for Leiden" help="Method for leiden (defaults to matrix which is fast for small datasets). Select iGraph to avoid casting large data to a dense matrix."> + <option value="matrix" selected="true">Matrix</option> + <option value="igraph">iGraph</option> + </param> + <param name="graph_name" argument="--graph-name" type="text" value="RNA_nn" label="Graph Name" help="Name of graph to use for the clustering algorith."/> + <param name="nrandom_starts" argument="--nrandom-starts" type="integer" optional="true" label="Random starts" help="Number of random starts, 10 by default."/> + <param name="group_singletons" argument="--group-singletons" type="boolean" truevalue="--group-singletons" falsevalue="" checked="false" label="Group singletons" help="Group singletons into nearest cluster. If FALSE, assign all singletons to a 'singleton' group."/> + <param name="random_seed" argument="--random-seed" type="integer" optional="true" label="Random seed" help="Seed of the random number generator"/> </section> + </inputs> <outputs> <!-- <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> --> - <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> + <expand macro="output_files"/> <data name="output_tab" format="csv" from_work_dir="output_tab" label="${tool.name} on ${on_string}: CSV Seurat Clusters"/> </outputs> @@ -72,7 +79,7 @@ <!-- Ensure count matrix input works --> <test> <param name="input" ftype="rdata" value="out_runpca.rds"/> - <output name="output" ftype="rdata" value="out_findclust.rds" compare="sim_size"/> + <output name="rds_seurat_file" ftype="rdata" value="out_findclust.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -80,16 +87,14 @@ **What it does** -Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. -It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and -interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse -types of single cell data. +Identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization +based clustering algorithm. First calculate k-nearest neighbors and construct t +he SNN graph (using Seurat find neighbours). +Then optimize the modularity function to determine clusters. +For a full description of the algorithms, see Waltman and van Eck (2013) +The European Physical Journal B. -Seurat clustering use SNN method to determine different clusters in your dataset. In order to construct a -SNN graph, you must have perform a PCA before launch this tool (you can use Seurat dimensional reduction). -It will search k (30) nearest neighbors for each cells and link cells to each other if they shared the -same neighbors. You can modulate the resolution in order to get larger (resolution superior to 1) or smaller -(inferior to 1) clusters. +@SEURAT_INTRO@ -----
--- a/seurat_macros.xml Wed Apr 03 11:17:04 2019 -0400 +++ b/seurat_macros.xml Mon Nov 25 06:09:15 2019 -0500 @@ -1,34 +1,110 @@ <?xml version="1.0"?> <macros> - - <token name="@VERSION@">0.0.5</token> - + <token name="@VERSION@">0.0.6</token> + <token name="@SEURAT_VERSION@">3.1.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">seurat-scripts</requirement> </requirements> </xml> - <xml name="version"> <version_command><![CDATA[ echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> </xml> + <xml name="input_object_params"> + <conditional name="input" label="Input format"> + <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData"> + <option value="rds_seurat" selected="true">RDS with a Seurat object</option> + <option value="loom">Loom</option> + <option value="anndata">AnnData</option> + <option value="rds_sce">RDS with a Single Cell Experiment object</option> + </param> + <when value="anndata"> + <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/> + </when> + <when value="loom"> + <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/> + </when> + <when value="rds_seurat"> + <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/> + </when> + <when value="rds_sce"> + <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/> + </when> + </conditional> + </xml> + + <token name="@INPUT_OBJECT@"> + #if $input.format == "anndata" + --input-object-file '$input.anndata_file' --input-format anndata + #else if $input.format == "loom" + --input-object-file '$input.loom_file' --input-format loom + #else if $input.format == "rds_seurat" + --input-object-file '$input.rds_seurat_file' --input-format seurat + #else if $input.format == "rds_sce" + --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment + #end if + </token> + + <xml name="output_object_params"> + <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom"> + <option value="rds_seurat" selected="true">RDS with a Seurat object</option> + <option value="loom">Loom</option> + <option value="rds_sce">RDS with a Single Cell Experiment object</option> + </param> + </xml> + + <xml name="output_files"> + <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom"> + <filter>format == 'loom'</filter> + </data> + <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS"> + <filter>format == 'rds_seurat'</filter> + </data> + <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS"> + <filter>format == 'rds_sce'</filter> + </data> + </xml> + + <token name="@OUTPUT_OBJECT@"> + #if $format == "anndata" + --output-object-file '$anndata_file' --output-format anndata + #else if $format == "loom" + --output-object-file seurat_obj.loom --output-format loom + #else if $format == "rds_seurat" + --output-object-file '$rds_seurat_file' --output-format seurat + #else if $format == "rds_sce" + --output-object-file '$rds_sce_file' --output-format singlecellexperiment + #end if + </token> + <xml name="genes-use-input"> - <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> + <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> </xml> <xml name="dims-use-input"> <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/> </xml> + <token name="@SEURAT_INTRO@"><![CDATA[ +Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. +It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and +interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse +types of single cell data. + ]]></token> + <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** -0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. +3.1.1_0.0.6+galaxy0: Moved to Seurat 3. + + Find clusters: removed dims-use, k-param, prune-snn. 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l). + +0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. ]]></token>