Mercurial > repos > ebi-gxa > ucsc_cell_browser
changeset 2:cc47d8df79eb draft default tip
"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 f12604f7ae850f2269a924f95a442c668948a61a"
author | ebi-gxa |
---|---|
date | Thu, 11 Jun 2020 20:58:35 +0000 |
parents | 92a98e92907f |
children | |
files | cell-browser.xml |
diffstat | 1 files changed, 8 insertions(+), 2 deletions(-) [+] |
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--- a/cell-browser.xml Fri May 29 11:09:28 2020 +0000 +++ b/cell-browser.xml Thu Jun 11 20:58:35 2020 +0000 @@ -1,7 +1,7 @@ -<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy1" profile="18.01"> +<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.7.10+galaxy0" 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> + <requirement type="package" version="0.7.10">ucsc-cell-browser</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -42,6 +42,11 @@ --markerField '${input_type.marker_field}' #end if + #if $input_type.cluster_field: + --clusterField '${input_type.cluster_field}' + #end if + + -o outdir -n sample --htmlDir '$html_file.extra_files_path'; cp '$__tool_directory__/redirect.html' '$html_file'; @@ -65,6 +70,7 @@ <when value="scanpy"> <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."/> + <param name="cluster_field" argument="--clusterField" type="text" label="Cluster field" help="Scanpy cluster field to use. Optional, if not set 'louvain' will be used. If the AnnData object doesn't not have 'louvain' among its clustering fields, then this NEEDS to be set or UCSC CellBrowser will fail."/> </when> </conditional> </inputs>