| Next changeset 1:bba8b14264c2 (2020-07-10) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f |
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README seurat_find_neighbours.xml seurat_macros.xml |
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| diff -r 000000000000 -r 4fff8ad1c76d README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Nov 25 06:07:31 2019 -0500 |
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| @@ -0,0 +1,1 @@ +Seurat tools |
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| diff -r 000000000000 -r 4fff8ad1c76d seurat_find_neighbours.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_find_neighbours.xml Mon Nov 25 06:07:31 2019 -0500 |
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| @@ -0,0 +1,128 @@ +<tool id="seurat_find_neighbours" name="Seurat FindNeighbours" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> + <description>constructs a Shared Nearest Neighbor (SNN) Graph</description> + <macros> + <import>seurat_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"><![CDATA[ +seurat-find-neighbours.R +@INPUT_OBJECT@ +$distance_matrix +#if $k_param + --k-param '$k_param' +#end if +$compute_snn +#if $prune_snn + --prune-snn '$prune_snn' +#end if +#if $nn_method + --nn-method '$nn_method' +#end if +#if $annoy_metric + --annoy-metric '$annoy_metric' +#end if +#if $graph_name + --graph-name '$graph_name' +#end if +#if $nn_eps and $nn_method == "rann" + --nn-eps '$nn_eps' +#end if +$force_recalc +#if $features_file + --features '$features_file' +#else if $features + --features '$features' +#end if +#if $reduction + --reduction '$reduction' +#end if +#if $dims + --dims '$dims' +#end if +#if $assay + --assay '$assay' +#end if +#if $do_plot + $do_plot +#end if +@OUTPUT_OBJECT@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param label="Features" optional="true" name="features" argument="--features" type="text" help="Comma-separated list of genes to use for building SNN."/> + <param label="Features file" optional="true" name="features_file" argument="--features" type="data" format="txt,tabular" help="Text file with one gene per line to use for building SNN. Overrides Features."/> + <param label="Plot SNN on tSNE" optional="true" name="do_plot" argument="--do-plot" type="boolean" truevalue="--do-plot" checked="false" help="Plot SNN graph on tSNE coordinates"/> + <param label="Reduction" optional="true" name="reduction" argument="--reduction" type="text" help="Reduction to use as input for building the SNN"/> + <param label="Dimensions" optional="true" name="dims" argument="--dims" type="text" help="Dimensions of reduction to use as input. A comma-separated list of the dimensions to use in construction of the SNN graph (e.g. To use the first 5 PCs, pass 1,2,3,4,5)."/> + <param label="Assay" optional="true" name="assay" argument="--assay" type="text" help="Assay to use in construction of SNN"/> + <param label="Distance matrix" optional="true" name="distance_matrix" argument="--distance-matrix" type="boolean" truevalue="--distance-matrix" falsevalue="" checked="false" help="Boolean value of whether the provided matrix is a distance matrix; note, for objects of class dist, this parameter will be set automatically."/> + <param label="k" optional="true" name="k_param" argument="--k-param" type="integer" help="Defines k for the k-nearest neighbor algorithm"/> + <param label="Compute SNN" optional="true" name="compute_snn" argument="--compute-snn" type="boolean" truevalue="--compute-snn" falsevalue="" checked="false" help="Also compute the shared nearest neighbor graph"/> + <param label="Prune SNN" optional="true" name="prune_snn" argument="--prune-snn" type="float" help="Sets the cutoff for acceptable Jaccard index 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)."/> + <param label="NN method" optional="true" name="nn_method" argument="--nn-method" type="select" help="Method for nearest neighbor finding. Options include: rann (default), annoy"> + <option value="rann" selected="true">rann</option> + <option value="annoy">annoy</option> + </param> + <param label="Annoy metric" optional="true" name="annoy_metric" argument="--annoy-metric" type="select" help="Distance metric for annoy. Options include: euclidean (default), cosine, manhattan, and hamming"> + <option value="euclidean" selected="true">Euclidean</option> + <option value="cosine">Cosine</option> + <option value="manhattan">Manhattan</option> + <option value="hamming">Hamming</option> + </param> + <param label="Graph name" optional="true" name="graph_name" argument="--graph-name" type="text" help="Name of graph to use for the clustering algorithm."/> + <param label="NN Error bound" optional="true" name="nn_eps" argument="--nn-eps" type="float" help="Error bound when performing nearest neighbor seach using RANN; default of 0.0 implies exact nearest neighbor search"/> + <param label="Force recalc" optional="true" name="force_recalc" argument="--force-recalc" type="boolean" truevalue="--force-recalc" falsevalue="" checked="false" help="Force recalculation of SNN"/> + </inputs> + + <outputs> + <expand macro="output_files"/> + <data name="snn_on_tsne" format="pdf" from_work_dir="snn_on_tsne.pdf" label="${tool.name} on ${on_string}: SNN on tSNE Plot"> + <filter>do_plot</filter> + </data> + </outputs> + + <tests> + <test> + <param name="input" ftype="rdata" value="seurat.rds"/> + <output name="rds_seurat_file" ftype="rdata" value="out_filter.rds" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Constructs a Shared Nearest Neighbor (SNN) Graph for a given dataset. +We first determine the k-nearest neighbors of each cell. We use this knn graph +to construct the SNN graph by calculating the neighborhood overlap (Jaccard index) +between every cell and its k.param nearest neighbors. + +@SEURAT_INTRO@ + +----- + +**Inputs** + + * Seurat RDS object. Probably the one produced by Seurat create object. + * Subset names. A list of attributes to subset on, colon separated (:). + * Low thresholds. A minimum value for each of the attributes set in subset names, again, colon separated (:). Optional. + * High thresholds. A maximum value for each of the attributes set in subset names, again, colon separated (:). Optional. + * Cells to use. A list of cell names/idenfifiers to filter positively by. + +----- + +**Outputs** + + * Seurat RDS object filtered according to the inputs. + +.. _Seurat: https://www.nature.com/articles/nbt.4096 +.. _Satija Lab: https://satijalab.org/seurat/ + +@VERSION_HISTORY@ + +]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 4fff8ad1c76d seurat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_macros.xml Mon Nov 25 06:07:31 2019 -0500 |
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| @@ -0,0 +1,126 @@ +<?xml version="1.0"?> +<macros> + <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,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** + +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> + + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.4096</citation> + <citation type="bibtex"> + @misc{r-seurat-scripts.git, + author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team}, + year = {2018}, + title = {Seurat-scripts: command line interface for Seurat}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, + } + </citation> + </citations> + </xml> +</macros> |