# HG changeset patch # User ebi-gxa # Date 1618702948 0 # Node ID 544d44faa8bf2d29861cf7a55078046464af22b1 # Parent 8da642e17794fb3af1762f30ec1f337c788dd509 "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 a0e5240b76fcf613ebe0a18b99ac29cdc95e073f" diff -r 8da642e17794 -r 544d44faa8bf cell-browser.xml --- a/cell-browser.xml Thu Jun 11 16:58:58 2020 -0400 +++ b/cell-browser.xml Sat Apr 17 23:42:28 2021 +0000 @@ -1,7 +1,7 @@ - + displays single-cell clusterized data in an interactive web application. - ucsc-cell-browser + ucsc-cell-browser @@ -18,7 +18,8 @@ cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path"; ## "sample" is used as name, so no change needed. - cp '$__tool_directory__/redirect.html' '$html_file'; + # cp '$__tool_directory__/redirect.html' '$html_file'; + mv '$redirect_html' '$html_file'; #else if $input_type.expression_source == "cell-browser-tar": @@ -28,7 +29,8 @@ ## 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' > '$html_file'; + ## sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file'; + sed "s/ds=sample/ds=\$study/" '$redirect_html' > '$html_file'; #else if $input_type.expression_source == "scanpy": @@ -48,10 +50,30 @@ -o outdir -n sample --htmlDir '$html_file.extra_files_path'; - cp '$__tool_directory__/redirect.html' '$html_file'; + ## cp '$__tool_directory__/redirect.html' '$html_file'; + mv '$redirect_html' '$html_file'; #end if ]]> + + + + + + + + Page Redirection + + + + If you are not redirected automatically, follow this link to example. + + + ]]> + @@ -69,8 +91,8 @@ - - + + @@ -78,10 +100,22 @@ + - - + + + + + + + + + + + + @@ -103,7 +137,14 @@ 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. +interactive site. + +For EBI Single Cell Expression Atlas AnnData files (available from http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/ + / .project.h5ad ), use `markers_louvain_resolution_` +for Marker genes fields and `louvain_resolution_` for Cluster field. There will be different +resolution values available, you can see them by executing `Inspect AnnData` tool, select +and set "What to inspect" to "General information about the object". Then look in the results under +obs and uns. Troubleshooting --------------- @@ -126,6 +167,9 @@ 0.5.38+galaxy0: Update UCSC CellBrowser version to 0.5.43. Fixes bugs and improves usage of gene symbols in AnnData objects. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + +1.0.0+galaxy0: Update UCSC CellBrowser version to 1.0.0. Fixes bugs and improves support for AnnData objects. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/. ]]> @@ -138,6 +182,7 @@ url = {https://github.com/maximilianh/cellBrowser}, } - 10.1101/2020.04.08.032698 + 10.1038/s41592-021-01102-w + 10.1101/2020.10.30.361162 diff -r 8da642e17794 -r 544d44faa8bf get_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_test_data.sh Sat Apr 17 23:42:28 2021 +0000 @@ -0,0 +1,3 @@ +#!/usr/bin/env bash +wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.project.h5ad +mv E-MTAB-6077.project.h5ad test-data/