| Previous changeset 1:265dcc5bc1e8 (2019-11-25) Next changeset 3:948ce48561f9 (2020-07-11) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0 |
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modified:
seurat_macros.xml seurat_read10x.xml |
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| diff -r 265dcc5bc1e8 -r 2d121013176f seurat_macros.xml --- a/seurat_macros.xml Mon Nov 25 06:10:49 2019 -0500 +++ b/seurat_macros.xml Fri Jul 10 21:48:16 2020 -0400 |
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| @@ -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> |
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| diff -r 265dcc5bc1e8 -r 2d121013176f seurat_read10x.xml --- a/seurat_read10x.xml Mon Nov 25 06:10:49 2019 -0500 +++ b/seurat_read10x.xml Fri Jul 10 21:48:16 2020 -0400 |
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| @@ -1,5 +1,5 @@ -<tool id="seurat_read10x" name="Seurat Read10x" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> -<description>Loads 10x data into a serialized seurat R object</description> +<tool id="seurat_read10x" name="Seurat Read10x" version="@SEURAT_VERSION@+galaxy1"> +<description>Loads Tabular or 10x data into a serialized seurat R object</description> <macros> <import>seurat_macros.xml</import> </macros> @@ -8,12 +8,19 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ -ln -s "$matrix" matrix.mtx; -ln -s "$genes" genes.tsv; -ln -s "$barcodes" barcodes.tsv; + +#if str($input.format) == "mtx": + ln -s "$matrix" matrix.mtx; + ln -s "$genes" genes.tsv; + ln -s "$barcodes" barcodes.tsv; +# end if -seurat-read-10x.R -d ./ - +seurat-read-10x.R +#if str($input.format) == "mtx": + -d ./ +#else + -f $input.file +# end if #if $metadata --metadata '$metadata' #end if @@ -28,9 +35,20 @@ ]]></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"/> + <conditional name="input" label="Input expression data"> + <param type="select" name="format" label="Choose the format of the input" help="10X MTX or tabular"> + <option value="mtx" selected="true">10X-type MTX</option> + <option value="tab" selected="true">tab-delimited text</option> + </param> + <when value="tab"> + <param type="data" name="file" label="Expression table" help="Tab-delimted expression table" format="tabular"/> + </when> + <when value="mtx"> + <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"/> + </when> + </conditional> <param label="Cell Metadata" optional="true" name="metadata" argument="--metadata" type="data" format="tsv,tabular" help="File with metdata for the cells, first column should be cell identifiers as used in the cells 10x file."/> <param label="Minimum cells to include features" optional="true" name="min_cells" argument="--min-cells" type="integer" help="Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff."/> <param label="Minimum features to include cells" optional="true" name="min_features" argument="--min-features" type="integer" help="Include cells where at least this many features are detected."/> @@ -57,9 +75,9 @@ @SEURAT_INTRO@ - **Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)** + **Read expression data from a tabular file or a 10x-Genomics-formatted mtx directory (`read_10x_mtx`)** - The mtx directory should contain: + For mtx, the 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. @@ -72,9 +90,10 @@ 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. + * A tabular file of expression data OR + * 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. * Optionally, a file with cell metadata. **Outputs** |