Mercurial > repos > ebi-gxa > scanpy_plot_embed

comparison scanpy-plot-embedding.xml @ 21:a71086d2e55f draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 64e51ed65585fdde84fb7463860dc559ffd36575-dirty"
author ebi-gxa
date Fri, 01 Oct 2021 13:37:30 +0000
parents 9fafbfcdee0d
children 35f6611fb8c3
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20:19124159e05a 21:a71086d2e55f
53 <valid initial="string.printable"/> 53 <valid initial="string.printable"/>
54 </sanitizer> 54 </sanitizer>
55 </param> 55 </param>
56 <param name="groups" argument="--groups" type="text" value="" label="Key for categorical in `.obs`" help="You can pass your predefined groups by choosing any categorical annotation of observations."/> 56 <param name="groups" argument="--groups" type="text" value="" label="Key for categorical in `.obs`" help="You can pass your predefined groups by choosing any categorical annotation of observations."/>
57 <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/> 57 <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
58 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/> 58 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes" help="Using this option means that scanpy will expect to find the raw data object. The job will fail if the raw data object is not present within the supplied AnnData file."/>
59 <param name="layer" argument="--layer" value="" type="text" 59 <param name="layer" argument="--layer" value="" type="text"
60 label="Name of the AnnData object layer to plot" help="By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw." /> 60 label="Name of the AnnData object layer to plot" help="By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw." />
61 <param name="neighbors_key" argument="--neighbors-key" value="" type="text" 61 <param name="neighbors_key" argument="--neighbors-key" value="" type="text"
62 label="Where to look for neighbors connectivities." help="If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities."/> 62 label="Where to look for neighbors connectivities." help="If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities."/>
63 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend"> 63 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">