| Previous changeset 2:e62673c32a5d (2019-12-05) Next changeset 4:a72e9faea895 (2019-12-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" |
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modified:
filter.xml macros.xml test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad |
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added:
test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png |
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| diff -r e62673c32a5d -r 0a6de5e65992 filter.xml --- a/filter.xml Thu Dec 05 07:14:15 2019 -0500 +++ b/filter.xml Thu Dec 12 09:28:18 2019 -0500 |
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| @@ -113,12 +113,12 @@ <expand macro="inputs_anndata"/> <conditional name="method"> <param argument="method" type="select" label="Method used for filtering"> - <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`</option> - <option value="pp.filter_genes">Filter genes based on number of cells or counts, using `pp.filter_genes`</option> - <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using `tl.filter_rank_genes_groups`</option> - <option value="pp.highly_variable_genes">, using `tl.highly_variable_genes`</option> - <option value="pp.subsample">Subsample to a fraction of the number of observations, using `pp.subsample`</option> - <option value="pp.downsample_counts">Downsample counts from count matrix, using `pp.downsample_counts`</option> + <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option> + <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option> + <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option> + <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option> + <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option> + <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option> </param> <when value="pp.filter_cells"> <conditional name="filter"> @@ -177,8 +177,8 @@ <when value="pp.highly_variable_genes"> <conditional name='flavor'> <param argument="flavor" type="select" label="Flavor for computing normalized dispersion"> - <option value="seurat">seurat: expects non-logarithmized data</option> - <option value="cell_ranger">cell_ranger: usually called for logarithmized data</option> + <option value="seurat">Seurat</option> + <option value="cell_ranger">Cell Ranger</option> </param> <when value="seurat"> <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/> @@ -191,7 +191,7 @@ </when> </conditional> <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/> - <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/> + <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/> </when> <when value="pp.subsample"> <conditional name="type"> @@ -200,7 +200,7 @@ <option value="n_obs">By number of observation</option> </param> <when value="fraction"> - <param argument="fraction" type="float" value="" label="Subsample to this `fraction` of the number of observations"/> + <param argument="fraction" type="float" value="" label="Subsample to this 'fraction' of the number of observations"/> </when> <when value="n_obs"> <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/> @@ -329,12 +329,14 @@ <param name="n_top_genes" value="2"/> </conditional> <param name="n_bins" value="20"/> + <param name="subset" value="true"/> </conditional> <assert_stdout> <has_text_matching expression="sc.pp.highly_variable_genes"/> <has_text_matching expression="flavor='cell_ranger'"/> <has_text_matching expression="n_top_genes=2"/> <has_text_matching expression="n_bins=20"/> + <has_text_matching expression="subset=True"/> </assert_stdout> <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/> </test> |
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| diff -r e62673c32a5d -r 0a6de5e65992 macros.xml --- a/macros.xml Thu Dec 05 07:14:15 2019 -0500 +++ b/macros.xml Thu Dec 12 09:28:18 2019 -0500 |
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| b'@@ -1,7 +1,7 @@\n <macros>\n <token name="@version@">1.4.4.post1</token>\n <token name="@profile@">19.01</token>\n- <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n+ <token name="@galaxy_version@"><![CDATA[@version@+galaxy1]]></token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@version@">scanpy</requirement>\n@@ -351,10 +351,10 @@\n <option value="gist_ncar">gist_ncar (Miscellaneous)</option>\n </xml>\n <xml name="param_groupby">\n- <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the heatmap is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into `num_categories`."/>\n+ <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into \'num_categories\'."/>\n </xml>\n <xml name="param_use_raw">\n- <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/>\n+ <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use \'raw\' attribute of input if present" help=""/>\n </xml>\n <xml name="param_log">\n <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>\n@@ -378,12 +378,12 @@\n <xml name="pl_var_names">\n <conditional name="var_names">\n <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >\n- <option value="all">All variables in `adata.var_names`</option>\n- <option value="custom">Subset of variables in `adata.var_names`</option>\n+ <option value="all">All variables in \'adata.var_names\'</option>\n+ <option value="custom">Subset of variables in \'adata.var_names\'</option>\n </param>\n <when value="all"/>\n <when value="custom">\n- <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of `adata.var_names`, and separated by comma"/>\n+ <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of \'adata.var_names\', and separated by comma"/>\n </when>\n </conditional>\n </xml>\n@@ -404,27 +404,20 @@\n <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>\n </xml>\n <xml name="param_layer">\n- <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" 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`."/>\n+ <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" 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\'."/>\n </xml>\n <token name="@CMD_param_plot_inputs@"><![CDATA[\n adata,\n save=\'.$format\',\n show=False,\n ]]></token>\n- <xml name="params_plots">\n+ <xml name="params_inputs">\n <expand macro="pl_var_names"/>\n <expand macro="param_groupby"/>\n- <expand macro="param_log"/>'..b'_pl_heatmap@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ show_gene_labels=$method.show_gene_labels,\n+ cmap=\'$method.matplotlib_pyplot_imshow.cmap\',\n+ #if str($method.matplotlib_pyplot_imshow.interpolation) != \'None\'\n+ interpolation=\'$method.matplotlib_pyplot_imshow.interpolation\',\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.alpha\n+ alpha=$method.matplotlib_pyplot_imshow.alpha,\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.vmin\n+ vmin=$method.matplotlib_pyplot_imshow.vmin,\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.vmax\n+ vmax=$method.matplotlib_pyplot_imshow.vmax,\n+ #end if\n+ origin=\'$method.matplotlib_pyplot_imshow.origin\'\n+ ]]>\n+ </token>\n+ <xml name="pl_rank_genes_groups_ext">\n+ <expand macro="param_groups"/>\n+ <expand macro="param_n_genes"/>\n+ <expand macro="param_key"/>\n+ </xml>\n+ <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[\n+ @CMD_params_groups@\n+ #if str($method.n_genes) != \'\'\n+ n_genes=$method.n_genes,\n+ #end if\n+ #if str($method.key) != \'\'\n+ key=\'$method.key\',\n+ #end if\n+ ]]>\n+ </token>\n+ <xml name="pl_matrixplot">\n+ <expand macro="param_swap_axes"/>\n+ <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">\n+ <param argument="cmap" type="select" label="Color palette">\n+ <expand macro="seaborn_color_palette_options"/>\n+ </param>\n+ <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>\n+ <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>\n+ <expand macro="param_matplotlib_pyplot_edgecolors"/>\n+ <expand macro="param_alpha"/>\n+ <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>\n+ </section>\n+ </xml>\n+ <token name="@CMD_pl_matrixplot@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ cmap=\'$method.matplotlib_pyplot_pcolor.cmap\',\n+ #if $method.matplotlib_pyplot_pcolor.vmin\n+ vmin=$method.matplotlib_pyplot_pcolor.vmin,\n+ #end if\n+ #if $method.matplotlib_pyplot_pcolor.vmax\n+ vmax=$method.matplotlib_pyplot_pcolor.vmax,\n+ #end if\n+ edgecolors=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n+ #if $method.matplotlib_pyplot_pcolor.alpha\n+ alpha=$method.matplotlib_pyplot_pcolor.alpha,\n+ #end if\n+ snap=$method.matplotlib_pyplot_pcolor.snap\n+ ]]>\n+ </token>\n+ <xml name="pl_stacked_violin">\n+ <expand macro="param_swap_axes"/>\n+ <section name="violin_plot" title="Violin plot attributes">\n+ <expand macro="conditional_stripplot"/>\n+ <expand macro="param_scale"/>\n+ </section>\n+ <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">\n+ <option value="muted">muted</option>\n+ <expand macro="seaborn_color_palette_options"/>\n+ </param>\n+ <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">\n+ <option value="None">No standardization</option>\n+ <option value="var">Standardization on variable</option>\n+ <option value="obs">Standardization on observation</option>\n+ </param>\n+ <expand macro="seaborn_violinplot"/>\n+ </xml>\n+ <token name="@CMD_pl_stacked_violin@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ @CMD_conditional_stripplot@\n+ scale=\'$method.violin_plot.scale\',\n+ row_palette=\'$method.row_palette\',\n+ #if str($method.standard_scale) != \'None\'\n+ standard_scale=\'$method.standard_scale\',\n+ #end if\n+ @CMD_params_seaborn_violinplot@\n+ ]]>\n+ </token>\n </macros>\n' |
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