Mercurial > repos > ebi-gxa > ucsc_cell_browser
changeset 3:ad5179780e25 draft
"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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
| author | ebi-gxa |
|---|---|
| date | Fri, 29 May 2020 07:09:58 -0400 |
| parents | 679dfd1dd63b |
| children | 8da642e17794 |
| files | cell-browser.xml redirect.html |
| diffstat | 2 files changed, 40 insertions(+), 8 deletions(-) [+] |
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--- a/cell-browser.xml Tue Aug 13 05:33:26 2019 -0400 +++ b/cell-browser.xml Fri May 29 07:09:58 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy0"> +<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy1" profile="18.01"> <description>displays single-cell clusterized data in an interactive web application.</description> <requirements> <requirement type="package" version="0.5.43">ucsc-cell-browser</requirement> @@ -9,26 +9,41 @@ <command><![CDATA[ #if $input_type.expression_source == "native-cell-browser": - echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE on WGCNA'} ]" > ./cellbrowser.conf; + echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE'} ]" > ./cellbrowser.conf; echo "meta = '$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"; + + ## "sample" is used as name, so no change needed. + cp '$__tool_directory__/redirect.html' '$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"; + + ## we need to adapt redirect to use the study name used in cellbrowser.conf + study=\$(grep '^name=' cellbrowser.conf | awk -F'=' '{ print $2 }' | sed s/\"//g ) && + echo "Study to replace: "\$study && + sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file'; #else if $input_type.expression_source == "scanpy": + ## We could add a condition here were, if cluster_field is provided + ## then we rename it inside with an AnnData relying script to read 'louvain' to please UCSC CellBrowser + ln -s '$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"; + cbImportScanpy -i scanpy_ann_data.h5ad + + #if $input_type.marker_field: + --markerField '${input_type.marker_field}' + #end if + + -o outdir -n sample --htmlDir '$html_file.extra_files_path'; + cp '$__tool_directory__/redirect.html' '$html_file'; #end if ]]></command> @@ -48,12 +63,13 @@ <param name="tarred_sources" type="data" format="tar" label="CellBrowser source files tarred" help="Tar containing CellBrowser config, tsne, umap and other source files for running cbBuild"/> </when> <when value="scanpy"> - <param name="input_anndata_file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/> + <param name="input_anndata_file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/> + <param name="marker_field" argument="--markerField" type="text" value="rank_genes_groups" label="Marker genes field" help="Scanpy marker genes field to use, optional, if not set 'rank_genes_groups' will be used."/> </when> </conditional> </inputs> <outputs> - <data format="html" name="html_file" label="Interactive UCSC Cell Browser"/> + <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/> </outputs> <tests> @@ -116,5 +132,6 @@ url = {https://github.com/maximilianh/cellBrowser}, } </citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/redirect.html Fri May 29 07:09:58 2020 -0400 @@ -0,0 +1,15 @@ +<!DOCTYPE HTML> +<html lang="en-US"> + <head> + <meta charset="UTF-8"> + <meta http-equiv="refresh" content="0; url=index.html?ds=sample"> + <script type="text/javascript"> + window.location.href = "index.html?ds=sample" + </script> + <title>Page Redirection</title> + </head> + <body> + <!-- Note: don't tell people to `click` the link, just tell them that it is a link. --> + If you are not redirected automatically, follow this <a href='index.html?ds=sample'>link to example</a>. + </body> +</html>