diff cluster_reduce_dimension.xml @ 7:b2df381a6004 draft

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

--- 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
@@ -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>