| Next changeset 1:265dcc5bc1e8 (2019-11-25) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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README seurat_macros.xml seurat_read10x.xml |
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| diff -r 000000000000 -r 1b8566f3c1d0 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Apr 03 11:18:21 2019 -0400 |
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| @@ -0,0 +1,1 @@ +Seurat tools |
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| diff -r 000000000000 -r 1b8566f3c1d0 seurat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_macros.xml Wed Apr 03 11:18:21 2019 -0400 |
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| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<macros> + + <token name="@VERSION@">0.0.5</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="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)."/> + </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="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. + +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). + ]]></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> |
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| diff -r 000000000000 -r 1b8566f3c1d0 seurat_read10x.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_read10x.xml Wed Apr 03 11:18:21 2019 -0400 |
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| @@ -0,0 +1,75 @@ +<tool id="seurat_read10x" name="Seurat Read10x" version="2.3.1+galaxy1"> +<description>Loads 10x data into a serialized seurat R object</description> + <macros> + <import>seurat_macros.xml</import> + </macros> + <expand macro="requirements" /> +<stdio> +<exit_code range="1:" /> +</stdio> +<command><![CDATA[ +ln -s "$matrix" matrix.mtx; +ln -s "$genes" genes.tsv; +ln -s "$barcodes" barcodes.tsv; + +seurat-read-10x.R -d ./ -o "$R_seurat_serialized" +]]></command> +<inputs> + <param type="data" name="matrix" help="Raw expression quantification as a sparse matrix in Matrix Market format, where each column is a gene and each row is a barcode/cell." format="txt" label="Expression matrix in sparse matrix format (.mtx)" /> + <param type="data" name="genes" help="Matrix market column file for genes" label="Gene table" format="tsv,tabular"/> + <param type="data" name="barcodes" help="Matrix market row file for genes" label="Barcode/cell table" format="tsv,tabular"/> +</inputs> +<outputs> + <data name="R_seurat_serialized" format="rdata" label="${tool.name} on ${on_string}: RData file" /> +</outputs> + +<tests> + <test> + <param name="matrix" ftype="txt" value="test_matrix.txt"/> + <param name="genes" ftype="txt" value="test_genes.txt"/> + <param name="barcodes" ftype="txt" value="test_barcodes.txt"/> + <output name="R_seurat_serialized" ftype="rdata" value="out_scale.rds" compare="sim_size"/> + </test> +</tests> + + +<help><![CDATA[ + .. class:: infomark + + **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. See the `Seurat Guided Clustering tutorial`_ for more information. + + **Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)** + + The mtx directory should contain: + + 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. + + 2) A gene table of at least two columns where the first column gives the gene IDs. + + 3) A barcode/cell table of at least one column giving the barcode/cell IDs. + + The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` + with a dataset accession. Otherwise, they need to be provided as separate Galaxy + datasets. + + **Inputs** + * Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. + * A gene table of at least two columns where the first column gives the gene IDs. + * A barcode/cell table of at least one column giving the barcode/cell IDs. + + **Outputs** + * R object for Seurat + + .. _Seurat: https://www.nature.com/articles/nbt.4096 + .. _Satija Lab: https://satijalab.org/seurat/ + .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html + +@VERSION_HISTORY@ +]]></help> +<expand macro="citations"/> +</tool> |