diff inspect.xml @ 7:6c145a6868cc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"

--- a/inspect.xml	Thu Feb 20 08:25:37 2020 -0500
+++ b/inspect.xml	Wed May 20 16:10:30 2020 -0400
@@ -41,7 +41,9 @@
             </param>
         </xml>
         <xml name="custom_penalty">
-            <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/>
+            <param argument="pen" type="text" value="" label="Norm used in the penalization" help="">
+                <expand macro="sanitize_query" />
+            </param>
         </xml>
         <xml name="random_state">
             <param argument="random_state" type="integer" value="" optional="true"
@@ -266,18 +268,26 @@
                 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option>
             </param>
             <when value="pp.calculate_qc_metrics">
-                <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X"/>
-                <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are"/>
-                <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"/>
+                <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are">
+                    <expand macro="sanitize_query" />
+                </param>
+                <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">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="percent_top" type="text" value="" label="Proportions of top genes to cover" 
-                    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"/>
+                    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">
+                    <expand macro="sanitize_vectors" />
+                </param>
             </when>
             <when value="pp.neighbors">
                 <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."/>
                 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
-                <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"/>
+                <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">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the 'n_neighbors' nearest neighbor."/>
                 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/>
                 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help="">
@@ -289,13 +299,19 @@
                 </param>
             </when>
             <when value="tl.score_genes">
-                <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma"/>
+                <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled"
                     help="If 'len(gene_list)' is not too low, you can set 'ctrl_size=len(gene_list)'."/>
                 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set"
-                    help="Default is all genes. Genes separated by a comma"/>
+                       help="Default is all genes. Genes separated by a comma">
+                    <expand macro="sanitize_query" />
+                </param>
                 <expand macro="score_genes_params"/>
-                <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'" help=""/>
+                <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'" help="">
+                    <expand macro="sanitize_query" />
+                </param>
             </when>
             <when value="tl.score_genes_cell_cycle">
                 <conditional name='s_genes'>
@@ -304,7 +320,9 @@
                         <option value="text" selected="true">Text</option>
                     </param>
                     <when value="text">
-                        <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma"/>
+                        <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma">
+                            <expand macro="sanitize_query" />
+                        </param>
                     </when>
                     <when value="file">
                         <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/>
@@ -316,7 +334,9 @@
                         <option value="text" selected="true">Text</option>
                     </param>
                     <when value="text">
-                        <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma"/>
+                        <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma">
+                            <expand macro="sanitize_query" />
+                        </param>
                     </when>
                     <when value="file">
                         <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/>
@@ -325,9 +345,13 @@
                 <expand macro="score_genes_params"/>
             </when>
             <when value="tl.rank_genes_groups">
-                <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help=""/>
+                <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help="">
+                    <expand macro="sanitize_query" />
+                </param>
                 <expand macro="param_use_raw"/>
-                <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."/>
+                <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.">
+                    <expand macro="sanitize_query" />
+                </param>
                 <conditional name="ref">
                     <param name="rest" type="select" label="Comparison">
                         <option value="rest">Compare each group to the union of the rest of the group</option>
@@ -335,7 +359,9 @@
                     </param>
                     <when value="rest"/>
                     <when value="group_id">
-                        <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"/>
+                        <param argument="reference" type="text" value="" label="Group identifier with respect to which compare">
+                            <expand macro="sanitize_query" />
+                        </param>
                     </when>
                 </conditional>
                 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>