| Previous changeset 6:f2f6c703da06 (2020-02-20) Next changeset 8:80d4e2cac903 (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 remove_confounders.xml |
| b |
| diff -r f2f6c703da06 -r 215733a383f2 macros.xml --- a/macros.xml Thu Feb 20 08:24:15 2020 -0500 +++ b/macros.xml Wed May 20 16:07:23 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' |
| b |
| diff -r f2f6c703da06 -r 215733a383f2 remove_confounders.xml --- a/remove_confounders.xml Thu Feb 20 08:24:15 2020 -0500 +++ b/remove_confounders.xml Wed May 20 16:07:23 2020 -0400 |
| b |
| @@ -72,19 +72,27 @@ <option value="pp.combat">Correct batch effects with ComBat function, using 'pp.combat'</option> </param> <when value="pp.regress_out"> - <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"/> + <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"> + <expand macro="sanitize_query" /> + </param> </when> <when value="pp.mnn_correct"> <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/> - <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used"/> - <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"/> + <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used"> + <expand macro="sanitize_query" /> + </param> + <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"> + <expand macro="sanitize_query" /> + </param> <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices"> <option value="-">-</option> <option value="_">_</option> <option value=" "> </option> <option value="/">/</option> </param> - <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key"/> + <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key"> + <expand macro="sanitize_query" /> + </param> <param argument="k" type="integer" value="20" label="Number of mutual nearest neighbors"/> <param argument="sigma" type="float" value="1" label="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors"/> <param argument="cos_norm_in" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed on the input data prior to calculating distances between cells?"/> @@ -92,7 +100,9 @@ <param argument="svd_dim" type="integer" value="" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch" help="If not set, biological components will not be removed from the correction vectors."/> <param argument="var_adj" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Adjust variance of the correction vectors?" help="This step takes most computing time."/> <param argument="compute_angle" type="boolean" truevalue="True" falsevalue="False" checked="false" label="compute the angle between each cell’s correction vector and the biological subspace of the reference batch?"/> - <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially"/> + <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially"> + <expand macro="sanitize_query" /> + </param> <param name="svd_mode" type="select" label="SVD mode"> <option value="svd">svd: SVD using a non-randomized SVD-via-ID algorithm</option> <option value="rsvd" selected="true">rsvd: SVD using a randomized SVD-via-ID algorithm</option> @@ -100,7 +110,9 @@ </param> </when> <when value="pp.combat"> - <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/> + <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"> + <expand macro="sanitize_query" /> + </param> </when> </conditional> <expand macro="inputs_common_advanced"/> |