| Previous changeset 6:5e9171dc8244 (2020-02-20) Next changeset 8:9d33775ec67d (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:
inspect.xml macros.xml |
| b |
| diff -r 5e9171dc8244 -r 6c145a6868cc inspect.xml --- a/inspect.xml Thu Feb 20 08:25:37 2020 -0500 +++ b/inspect.xml Wed May 20 16:10:30 2020 -0400 |
| [ |
| b'@@ -41,7 +41,9 @@\n </param>\n </xml>\n <xml name="custom_penalty">\n- <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/>\n+ <param argument="pen" type="text" value="" label="Norm used in the penalization" help="">\n+ <expand macro="sanitize_query" />\n+ </param>\n </xml>\n <xml name="random_state">\n <param argument="random_state" type="integer" value="" optional="true"\n@@ -266,18 +268,26 @@\n <option value="pp.sqrt">Square root the data matrix, using \'pp.sqrt\'</option>\n </param>\n <when value="pp.calculate_qc_metrics">\n- <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X"/>\n- <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are"/>\n- <param argument="qc_vars" type="text" value="" label="Keys for boolean columns of \'.var\' which identify variables you could want to control for" \n- help="Keys separated by a comma"/>\n+ <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are">\n+ <expand macro="sanitize_query" />\n+ </param>\n+ <param argument="qc_vars" type="text" value="" label="Keys for boolean columns of \'.var\' which identify variables you could want to control for" help="Keys separated by a comma">\n+ <expand macro="sanitize_query" />\n+ </param>\n <param argument="percent_top" type="text" value="" label="Proportions of top genes to cover" \n- help=" Values (integers) are considered 1-indexed, \'50\' finds cumulative proportion to the 50th most expressed genes. Values separated by a comma. \n- If empty don\'t calculate"/>\n+ help=" Values (integers) are considered 1-indexed, \'50\' finds cumulative proportion to the 50th most expressed genes. Values separated by a comma. If empty don\'t calculate">\n+ <expand macro="sanitize_vectors" />\n+ </param>\n </when>\n <when value="pp.neighbors">\n <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If \'knn\' is \'True\', number of nearest neighbors to be searched. If \'knn\' is \'False\', a Gaussian kernel width is set to the distance of the \'n_neighbors\' neighbor."/>\n <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>\n- <param argument="use_rep" type="text" value="" optional="true" label="Indicated representation to use" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it\'s computed with default parameter"/>\n+ <param argument="use_rep" type="text" value="" optional="true" label="Indicated representation to use" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it\'s computed with default parameter">\n+ <expand macro="sanitize_query" />\n+ </param>\n <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the '..b'ument="score_name" type="text" value="score" label="Name of the field to be added in \'.obs\'" help=""/>\n+ <param argument="score_name" type="text" value="score" label="Name of the field to be added in \'.obs\'" help="">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n <when value="tl.score_genes_cell_cycle">\n <conditional name=\'s_genes\'>\n@@ -304,7 +320,9 @@\n <option value="text" selected="true">Text</option>\n </param>\n <when value="text">\n- <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma"/>\n+ <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n <when value="file">\n <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/>\n@@ -316,7 +334,9 @@\n <option value="text" selected="true">Text</option>\n </param>\n <when value="text">\n- <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma"/>\n+ <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n <when value="file">\n <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/>\n@@ -325,9 +345,13 @@\n <expand macro="score_genes_params"/>\n </when>\n <when value="tl.rank_genes_groups">\n- <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help=""/>\n+ <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help="">\n+ <expand macro="sanitize_query" />\n+ </param>\n <expand macro="param_use_raw"/>\n- <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. [\'g1\', \'g2\', \'g3\']. If not passed, a ranking will be generated for all groups."/>\n+ <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. [\'g1\', \'g2\', \'g3\']. If not passed, a ranking will be generated for all groups.">\n+ <expand macro="sanitize_query" />\n+ </param>\n <conditional name="ref">\n <param name="rest" type="select" label="Comparison">\n <option value="rest">Compare each group to the union of the rest of the group</option>\n@@ -335,7 +359,9 @@\n </param>\n <when value="rest"/>\n <when value="group_id">\n- <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"/>\n+ <param argument="reference" type="text" value="" label="Group identifier with respect to which compare">\n+ <expand macro="sanitize_query" />\n+ </param>\n </when>\n </conditional>\n <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>\n' |
| b |
| diff -r 5e9171dc8244 -r 6c145a6868cc macros.xml --- a/macros.xml Thu Feb 20 08:25:37 2020 -0500 +++ b/macros.xml Wed May 20 16:10:30 2020 -0400 |
| [ |
| 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' |