| Next changeset 1:674777a022e4 (2019-06-05) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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cell-browser.xml |
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| diff -r 000000000000 -r 1b43a2d812c9 cell-browser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cell-browser.xml Wed Apr 03 11:56:43 2019 -0400 |
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| @@ -0,0 +1,114 @@ +<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.4.38+galaxy0"> + <description>displays single-cell clusterized data in an interactive web application.</description> + <requirements> + <requirement type="package" version="0.4.38">ucsc-cell-browser</requirement> + </requirements> +<stdio> +<exit_code range="1:" /> +</stdio> +<command><![CDATA[ +#if $input_type.expression_source == "native-cell-browser": + + echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE on WGCNA'} ]" > ./cellbrowser.conf; + echo "meta = '$cellMetadata'" >> ./cellbrowser.conf; + echo "name = 'sample'" >> ./cellbrowser.conf; + echo "exprMatrix = '$expressionMatrix'" >> ./cellbrowser.conf; + echo "geneIdType = 'symbol'" >> ./cellbrowser.conf; + + cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path"; + mv "$html_file.extra_files_path"/index.html "$html_file"; + +#else if $input_type.expression_source == "cell-browser-tar": + + tar -xf '$tarred_sources'; + cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path"; + mv "$html_file.extra_files_path"/index.html "$html_file"; + +#else if $input_type.expression_source == "scanpy": + + ln -s '$input_anndata_file' scanpy_ann_data.h5ad; + cbImportScanpy -i scanpy_ann_data.h5ad -o outdir -n sample --htmlDir "$html_file.extra_files_path"; + mv "$html_file.extra_files_path"/index.html "$html_file"; + +#end if +]]></command> +<inputs> + <conditional name="input_type"> + <param type="select" name="expression_source" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects"> + <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option> + <option value="scanpy">Scanpy AnnData HDF5 serialized object</option> + <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option> + </param> + <when value="native-cell-browser"> + <param type="data" name="expressionMatrix" label="Expression matrix" help="Tabular expression matrix (see https://github.com/maximilianh/cellBrowser/tree/master/sampleData)" format="tabular"/> + <param type="data" name="cellMetadata" label="Cell metadata" help="Tabular file with metadata fields (columns) for each cell (rows)." format="tabular"/> + <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/> + </when> + <when value="cell-browser-tar"> + <param name="tarred_sources" type="data" format="tar" label="CellBrowser source files tarred" help="Tar containing CellBrowser config, tsne, umap and other source files for running cbBuild"/> + </when> + <when value="scanpy"> + <param name="input_anndata_file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/> + </when> + </conditional> +</inputs> +<outputs> + <data format="html" name="html_file" label="Interactive UCSC Cell Browser"/> +</outputs> + +<tests> + <test> + <param name="input_anndata_file" ftype="data" value="anndata.h5"/> + <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/> + </test> +</tests> + +<help><![CDATA[ +UCSC Single Cell Browser +======================== + +Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg +Initiative https://www.chanzuckerberg.com/. + +The UCSC Cell Browser is a viewer for single cell data. You can click on and hover +over cells to get meta information, search for genes to color on and click clusters +to show cluster-specific marker genes, which in turn are clickable again. + +For a demo of the browser, see http://cells.ucsc.edu + +Usage +----- + +After choosing the inputs and executing the tool, once the history item becomes +green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser +interactive site. Press the white on blue "Open Dataset" button. + +Troubleshooting +--------------- + +Depending on the window size when pressing the "View data" button, you might see a black canvas and a diminished panel to the upper left +with the text "Choose cell...". If that is the case, close that panel (click on the cross) +and then choose File -> Open Dataset... and then press the Open Dataset white button. + +Version history +--------------- + +0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/. + +0.4.38+galaxy0: Supports Seurat (through a converter) and Scanpy input. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/. +]]></help> +<citations> + <citation type="bibtex"> + @misc{ucsc-cell-browser-gitrepo, + author = {Maximilian Haeussler and collaborators}, + year = {2018}, + title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/maximilianh/cellBrowser}, + } + </citation> +</citations> +</tool> |