| Previous changeset 6:77b91b9bdf52 (2020-02-20) Next changeset 8:35bc2eb568ed (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:
cluster_reduce_dimension.xml macros.xml |
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| diff -r 77b91b9bdf52 -r b2df381a6004 cluster_reduce_dimension.xml --- a/cluster_reduce_dimension.xml Thu Feb 20 08:23:29 2020 -0500 +++ b/cluster_reduce_dimension.xml Wed May 20 16:11:15 2020 -0400 |
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| @@ -4,7 +4,9 @@ <import>macros.xml</import> <xml name="pca_inputs"> <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/> - <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""/> + <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""> + <expand macro="sanitize_query" /> + </param> <conditional name="pca"> <param argument="chunked" type="select" label="Type of PCA?"> <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of 'random_seed' and 'svd_solver')</option> @@ -210,14 +212,18 @@ <when value="igraph"/> </conditional> <expand macro="param_random_state"/> - <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""/> + <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""> + <expand macro="sanitize_query" /> + </param> <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/> <expand macro="param_use_weights"/> </when> <when value="tl.leiden"> <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/> <expand macro="param_random_state"/> - <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help=""/> + <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help=""> + <expand macro="sanitize_query" /> + </param> <expand macro="param_use_weights"/> <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/> </when> @@ -257,9 +263,13 @@ <expand macro="param_layout"/> <expand macro="param_root"/> <expand macro="param_random_state"/> - <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)"/> + <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)"> + <expand macro="sanitize_query" /> + </param> <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/> - <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'"/> + <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'"> + <expand macro="sanitize_query" /> + </param> </when> <when value="tl.dpt"> <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/> @@ -268,7 +278,9 @@ <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/> </when> <when value="tl.paga"> - <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs')."/> + <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs')."> + <expand macro="sanitize_query" /> + </param> <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/> <param argument="model" type="select" label="PAGA connectivity model" help=""> <option value="v1.2">v1.2</option> |
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| diff -r 77b91b9bdf52 -r b2df381a6004 macros.xml --- a/macros.xml Thu Feb 20 08:23:29 2020 -0500 +++ b/macros.xml Wed May 20 16:11:15 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' |