| Previous changeset 10:068c4bf0e0db (2020-06-05) Next changeset 12:e9f7c33e2b46 (2020-09-10) |
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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/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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modified:
scanpy-plot-embedding.xml scanpy_macros2.xml |
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| diff -r 068c4bf0e0db -r f48cfaa2e515 scanpy-plot-embedding.xml --- a/scanpy-plot-embedding.xml Fri Jun 05 08:55:24 2020 -0400 +++ b/scanpy-plot-embedding.xml Mon Sep 07 14:02:08 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>visualise cell embeddings</description> <macros> <import>scanpy_macros2.xml</import> @@ -8,31 +8,58 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli plot embed - @INPUT_OPTS@ - --basis '${basis}' +@INPUT_OPTS@ +#if $color_by --color '${color_by}' - ${use_raw} +#end if +${use_raw} --legend-loc '${legend_loc}' --legend-fontsize '${legend_fontsize}' +#if $basis + --basis '${basis}' +#end if +#if $groups + --groups $groups +#end if +#if $neighbors_key + --neighbors-key '${neighbors_key}' +#end if +#if $layer + --layer '${layer}' +#end if #if $point_size --size ${point_size} #end if #if $gene_symbols_field --gene-symbols ${gene_symbols_field} + #end if +${edges} --edges-width ${edges_width} +#if $edges_color + --edges-color ${edges_color} #end if - @PLOT_OPTS@ +#if $components + --components ${components} +#end if +--projection $projection +$sort_order +@PLOT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> - <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/> - <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"> + <param name="basis" argument="--basis" type="text" value='umap' label="name of the embedding to plot"/> + <param name="color_by" argument="--color" type="text" label="color by attributes, comma separated texts"> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> + <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."/> <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'"/> <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/> + <param name="layer" argument="--layer" value="" type="text" + 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." /> + <param name="neighbors_key" argument="--neighbors-key" value="" type="text" + 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."/> <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend"> <option value="right margin" selected="true">Right margin</option> <option value="on data">On data</option> @@ -40,6 +67,15 @@ <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/> <param name="point_size" argument="--size" type="integer" optional="true" label="Point size" help="Automatically determined if not specified."/> + <param name="edges" argument="--edges" type="boolean" checked="False" truevalue="--edges" falsevalue="" label="Show edges?"/> + <param name="edges_width" argument="--edges-width" type="float" value="0.1" label="Width of edges"/> + <param name="edges_color" argument="--edges-color" type="text" value="" label="Color of edges"/> + <param name="sort_order" argument="--no-sort-order" type="boolean" checked="False" truevalue="" falsevalue="--no-sort-order" label="Plot in order?" help="For continuous annotations used as 'color parameter, plot data points with higher values on top of others."/> + <param name="components" argument="--components" type="text" value="" label="Components to plot" help="Comma-separated list, e.g. '1,2', '2,3'. To plot all available components use 'all'."/> + <param name="projection" argument="--projection" type="select" label="Plot projection"> + <option value="2d" selected="true">2D</option> + <option value="3d">3D</option> + </param> <expand macro="output_plot_params"/> </inputs> @@ -51,8 +87,9 @@ <test> <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> + <param name="basis" value="X_pca"/> <param name="color_by" value="louvain"/> - <output name="output_png" file="run_tsne.png" ftype="png" compare="sim_size"/> + <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/> </test> </tests> |
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| diff -r 068c4bf0e0db -r f48cfaa2e515 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 08:55:24 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 14:02:08 2020 +0000 |
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| @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> |