| Previous changeset 6:dbbe1ea8ecb1 (2020-02-20) Next changeset 8:6adf98e782f3 (2021-03-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" |
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modified:
macros.xml plot.xml |
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| diff -r dbbe1ea8ecb1 -r 7647e5cd1b8b macros.xml --- a/macros.xml Thu Feb 20 08:22:46 2020 -0500 +++ b/macros.xml Wed May 20 16:08:18 2020 -0400 |
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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@+galaxy2]]></token>\n+ <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@version@">scanpy</requirement>\n@@ -37,6 +37,20 @@\n import numpy as np\n ]]>\n </token>\n+ <xml name="sanitize_query" token_validinitial="string.printable">\n+ <sanitizer>\n+ <valid initial="@VALIDINITIAL@">\n+ <remove value="'" />\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+ <xml name="sanitize_vectors" token_validinitial="string.digits">\n+ <sanitizer>\n+ <valid initial="@VALIDINITIAL@">\n+ <add value=","/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n <xml name="inputs_anndata">\n <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>\n </xml>\n@@ -368,7 +382,9 @@\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 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+ <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+ <expand macro="sanitize_query" />\n+ </param>\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@@ -400,7 +416,9 @@\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+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n </conditional>\n </xml>\n@@ -414,14 +432,18 @@\n <repeat name="var_group_positions" title="Group of variables to highlight" help="This will draw a \'bracket\' on top of the plot between the given start and end positions. If a label is given, it will be added on top of the bracket. ">\n <param name="start" type="integer" min="0" value="" label="Start" help=""/>\n <param name="end" type="integer" min="0" value="" label="End" help=""/>\n- <param argument="label" type="text" value="" label="Label" help=""/>\n+ <param argument="label" type="text" value="" label="Label" help="">\n+ <expand macro="sanitize_query" />\n+ </param>\n </repeat>\n </xml>\n <xml name="param_var_group_rotation">\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 t'..b'nal="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/>\n- <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which \'tl.paga\' has been computed."/>\n+ <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which \'tl.paga\' has been computed.">\n+ <expand macro="sanitize_query" />\n+ </param>\n <expand macro="param_layout"/>\n <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/>\n <expand macro="param_random_state"/>\n <expand macro="param_root"/>\n- <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for \'.uns[\'paga\']\', e.g. \'transistions_confidence\'"/>\n- <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga"/>\n- <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn."/>\n+ <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for \'.uns[\'paga\']\', e.g. \'transistions_confidence\'">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn.">\n+ <expand macro="sanitize_query" />\n+ </param>\n <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>\n <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>\n <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>\n@@ -1066,7 +1110,9 @@\n <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains \'var_names\' (e.g. genes) and the y axis the \'groupby\' categories (if any). By setting \'swap_axes\' then x are the \'groupby\' categories and y the \'var_names\'."/>\n </xml>\n <xml name="gene_symbols">\n- <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in \'.var\' that stores gene symbols"/>\n+ <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in \'.var\' that stores gene symbols">\n+ <expand macro="sanitize_query" />\n+ </param>\n </xml>\n <xml name="param_n_genes">\n <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>\n@@ -1091,7 +1137,9 @@\n ]]>\n </token>\n <xml name="param_key">\n- <param argument="key" type="text" value="" label="Key used to store the ranking results in \'uns\'"/>\n+ <param argument="key" type="text" value="" label="Key used to store the ranking results in \'uns\'">\n+ <expand macro="sanitize_query" />\n+ </param>\n </xml>\n <xml name="pl_heatmap">\n <expand macro="param_swap_axes"/>\n' |
| b |
| diff -r dbbe1ea8ecb1 -r 7647e5cd1b8b plot.xml --- a/plot.xml Thu Feb 20 08:22:46 2020 -0500 +++ b/plot.xml Wed May 20 16:08:18 2020 -0400 |
| b |
| b'@@ -25,6 +25,9 @@\n #if $method.type.type == \'xy\'\n x=\'$method.type.x\',\n y=\'$method.type.y\',\n+ #if str($method.type.color) != \'\'\n+ color=\'$method.type.color\',\n+\t #end if\n #if str(\'$method.type.layers.use_layers\') == \'true\'\n layers=(\'$method.type.layers.layer_x\', \'$method.type.layers.layer_y\', \'$method.type.layers.layer_color\'),\n #end if\n@@ -41,15 +44,17 @@\n @CMD_params_pl_components@\n projection=\'$method.plot.projection\',\n legend_loc=\'$method.plot.legend_loc\',\n+ #if $method.plot.palette != \'default\'\n+ palette=\'$method.plot.palette\',\n+ #end if\n+ #if $method.plot.color_map != \'None\'\n+ color_map=\'$method.plot.color_map\',\n+ #end if\n @CMD_param_legend_fontsize@\n legend_fontweight=\'$method.plot.legend_fontweight\',\n- color_map=\'$method.plot.color_map\',\n- #if str($method.plot.palette) != \'\'\n- palette=\'$method.plot.palette\',\n- #end if\n- frameon=$method.plot.frameon,\n @CMD_param_title@\n- @CMD_param_size@)\n+ @CMD_param_size@\n+ frameon=$method.plot.frameon)\n \n #else if $method.method == \'pl.heatmap\'\n sc.pl.heatmap(\n@@ -412,17 +417,30 @@\n <option value="basis">Using tool that computes coordinates</option>\n </param>\n <when value="xy">\n- <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either \'.obs\' or \'.var\'"/>\n- <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either \'.obs\' or \'.var\'"/>\n+ <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either \'.obs\' or \'.var\'">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either \'.obs\' or \'.var\'">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">\n+ <expand macro="sanitize_query" />\n+ </param>\n <conditional name="layers">\n <param argument="use_layers" type="select" label="Use the layers attribute?">\n <option value="true">Yes</option>\n <option value="false" selected="true">No</option>\n </param>\n <when value="true">\n- <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the \'layers\' attribute of \'adata\' if present"/>\n- <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the \'layers\' attribute of \'adata\' if present"/>\n- <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the \'layers\' attribute of \'adata\' if present"/>\n+ <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the \'layers\' attribute of \'adata\' if present">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the \'layers\' attribute of \'adata\' if present">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the \'layers\' attribute'..b' <expand macro="section_matplotlib_pyplot_scatter"/>\n </when>\n <when value="pl.pca_loadings">\n- <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>\n+ <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n <when value="pl.pca_variance_ratio">\n <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>\n@@ -642,13 +672,21 @@\n </when>\n <when value="pl.paga_path">\n <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"\n- help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>\n- <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from \'.var_names\' or fields of \'.obs\'"/>\n+ help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from \'.var_names\' or fields of \'.obs\'">\n+ <expand macro="sanitize_query" />\n+ </param>\n <expand macro="param_use_raw"/>\n- <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>\n+ <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated">\n+ <expand macro="sanitize_query" />\n+ </param>\n <expand macro="param_color_map"/>\n <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>\n- <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/>\n+ <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">\n+ <expand macro="sanitize_query" />\n+ </param>\n <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>\n <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>\n <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>\n@@ -674,7 +712,9 @@\n <expand macro="param_n_genes"/>\n </when>\n <when value="gene_names">\n- <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/>\n+ <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n </conditional>\n <expand macro="gene_symbols"/>\n' |