| Previous changeset 2:8e0f141c8c66 (2019-12-05) Next changeset 4:55f2212bb675 (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:
macros.xml normalize.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 8e0f141c8c66 -r d7ea9b5e6df1 macros.xml --- a/macros.xml Thu Dec 05 07:12:40 2019 -0500 +++ b/macros.xml Thu Dec 12 09:27:00 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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| diff -r 8e0f141c8c66 -r d7ea9b5e6df1 normalize.xml --- a/normalize.xml Thu Dec 05 07:12:40 2019 -0500 +++ b/normalize.xml Thu Dec 12 09:27:00 2019 -0500 |
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| @@ -23,11 +23,15 @@ #if $method.exclude_highly_expressed.exclude_highly_expressed == "True" max_fraction=$method.exclude_highly_expressed.max_fraction, #end if + #if str($method.key_added) != '' key_added='$method.key_added', - #if str($method.layers) != 'all' + #end if + #if str($method.layers) != '' + #if str($method.layers) != 'all' layers[str(x.strip()) for x in str($method.layers).split(',')], - #else + #else layers='$method.layers', + #end if #end if #if str($method.layer_norm) != "None" layer_norm='$method.layer_norm', @@ -70,10 +74,10 @@ <expand macro="inputs_anndata"/> <conditional name="method"> <param argument="method" type="select" label="Method used for normalization"> - <option value="pp.normalize_total">Normalize counts per cell, using `pp.normalize_total`</option> - <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17`</option> - <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17`</option> - <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat`</option> + <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option> + <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option> + <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option> + <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option> </param> <when value="pp.normalize_total"> <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/> @@ -87,8 +91,8 @@ </when> <when value="False"/> </conditional> - <param argument="key_added" type="text" value="n_counts" label="Name of the field in `adata.obs` where the normalization factor is stored" help=""/> - <param argument="layers" type="text" value="all" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/> + <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help=""/> + <param argument="layers" type="text" value="" optional="true" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/> <param argument="layer_norm" type="select" label="How to normalize layers?"> <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option> <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option> |
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