Mercurial > repos > ebi-gxa > seurat_scale_data
changeset 1:3d0bfc2a233e 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 06:11:23 -0500 |
parents | 6166efaeb4a6 |
children | 1a8e93921f01 |
files | seurat_macros.xml seurat_scale_data.xml |
diffstat | 2 files changed, 101 insertions(+), 25 deletions(-) [+] |
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--- a/seurat_macros.xml Wed Apr 03 11:18:45 2019 -0400 +++ b/seurat_macros.xml Mon Nov 25 06:11:23 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>
--- a/seurat_scale_data.xml Wed Apr 03 11:18:45 2019 -0400 +++ b/seurat_scale_data.xml Mon Nov 25 06:11:23 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="seurat_scale_data" name="Seurat ScaleData" version="2.3.1+galaxy1"> +<tool id="seurat_scale_data" name="Seurat ScaleData" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> <description>scale and center genes</description> <macros> <import>seurat_macros.xml</import> @@ -8,21 +8,21 @@ <command detect_errors="exit_code"><![CDATA[ seurat-scale-data.R ---input-object-file '$input' +@INPUT_OBJECT@ #if $vars: --vars-to-regress '$vars' #else --vars-to-regress nUMI #end if -#if $genes: - --genes-use '$genes' +#if $genes_use: + --genes-use '$genes_use' #end if --model-use '$model' $use_umi -$do_center +$do_not_center #if $scale_max: --scale-max '$scale_max' @@ -38,22 +38,26 @@ $check_for_norm - - ---output-object-file '$output' +@OUTPUT_OBJECT@ ]]></command> <inputs> - <param name="input" argument="--input-object-file" type='data' format='rdata' help="File name in where a serialized R matrix object can be found." label="Seurat RDS object"/> - <param name="genes" argument="--genes-use" type='data' format='txt' optional='true' help="File to be used to derive a vector of gene names to scale/center (one gene per line). Default is all genes in object@data."/> - <param name="vars" argument="--vars-to-regress" type='text' optional='True' label="Vars to regress" help="Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito."/> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <expand macro="genes-use-input"/> + <param name="vars" argument="--vars-to-regress" type='text' value="nCount_RNA" label="Vars to regress" help="Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nCount_RNA, or percent.mito."> + <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator> + <option value="nCount_RNA">nCount_RNA</option> + <option value="nFeature_RNA">nFeature_RNA</option> + </param> <param name="model" argument="--model-use" type="select" label="Statistical model" help="Use a linear model or generalized linear model (poisson, negative binomial) for the regression."> <option value="linear" selected="true">Linear model</option> <option value="poisson">Poisson model</option> <option value="negbinom">Negative binomial model</option> </param> <param name="use_umi" argument="--use-umi" type="boolean" truevalue="--use-umi TRUE" falsevalue="" checked="false" label="Use UMIs." help="Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'."/> - <param name="do_center" argument="--do-center" type="boolean" falsevalue="--do-center FALSE" truevalue="" checked="true" label="Perform centering" help="Whether to center the data."/> + <param name="do_not_center" argument="--do-not-center" type="boolean" falsevalue="" truevalue="--do-not-center" checked="false" label="Skip centering" help="By default data is centered, with this option you can skip centering."/> + <param name="do_not_scale" argument="--do-not-scale" type="boolean" falsevalue="" truevalue="--do-not-scale" checked="false" label="Skip scaling" help="By default data is scaled, with this option you can skip scaling."/> <param name="scale_max" argument="--scale-max" optional="true" type="float" label="Scale maximum" help = "Max value to return for scaled data. The default is 10. Setting this can help reduce the effects of genes that are only expressed in a very small number of cells. If regressing out latent variables and using a non-linear model, the default is 50."/> <param name="block_size" argument="--block-size" optional="true" type="integer" label="Block size" help = "Default size for number of genes to scale at in a single computation. Increasing block.size may speed up calculations but at an additional memory cost. Defaults to 1000 if not specified."/> <param name="min_cells_to_block" argument="--min-cells-to-block" optional="true" type="integer" label="Minimum number of cells to block" help="If object contains fewer than this number of cells, don't block for scaling calculations. Defaults to 1000."/> @@ -61,13 +65,13 @@ </inputs> <outputs> - <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> + <expand macro="output_files"/> </outputs> <tests> <test> <param name="input" ftype="rdata" value="out_findvar.rds"/> - <output name="output" ftype="rdata" value="out_scale.rds" compare="sim_size"/> + <output name="rds_seurat_file" ftype="rdata" value="out_scale.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -75,13 +79,9 @@ **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. - This tool regresses out variables in a Seurat object to mitigate the effect of confounding factors. +@SEURAT_INTRO@ -----