diff inspect.xml @ 12:3081ff5c84a3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0

--- a/inspect.xml	Wed Nov 08 14:48:14 2023 +0000
+++ b/inspect.xml	Fri Nov 17 09:15:15 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -66,11 +66,11 @@
     adata=adata,
     expr_type='$method.expr_type',
     var_type='$method.var_type',
-    #if str($method.qc_vars) != ''
+    #if $method.qc_vars
         #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
     qc_vars=$qc_vars,
     #end if
-    #if str($method.percent_top) != ''
+    #if $method.percent_top
         #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
         percent_top=$method.percent_top,
     #end if
@@ -125,7 +125,7 @@
     #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
-    #if str($method.use_rep) != ''
+    #if $method.use_rep
     use_rep='$method.use_rep',
     #end if
     knn=$method.knn,
@@ -138,7 +138,7 @@
 sc.tl.rank_genes_groups(
     adata=adata,
     groupby='$method.groupby',
-    #if str($method.groups) != ''
+    #if $method.groups
     #set $group=[x.strip() for x in str($method.groups).split(',')]
     groups=$group,
     #end if
@@ -176,13 +176,13 @@
             #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
     intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
             #end if
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
         #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
     penalty='l2',
     fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
     max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
@@ -213,7 +213,7 @@
 sc.tl.marker_gene_overlap(
     adata,
     reference_markers,
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     method='$method.overlap.method',
@@ -226,7 +226,7 @@
     #if str($method.adj_pval_threshold) != ''
     adj_pval_threshold=$method.adj_pval_threshold,
     #end if
-    #if str($method.key_added) != ''
+    #if $method.key_added
     key_added='$method.key_added',
     #end if
     inplace=True)
@@ -240,7 +240,7 @@
 sc.pp.scale(
     adata,
     zero_center=$method.zero_center,
-    #if $method.max_value
+    #if str($method.max_value) != ''
     max_value=$method.max_value,
     #end if
     copy=False)
@@ -368,9 +368,9 @@
                 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
                 <conditional name="tl_rank_genes_groups_method">
                     <param argument="method" type="select" label="Method">
-                        <option value="t-test">t-test</option>
+                        <option value="t-test" selected="true">t-test</option>
                         <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
-                        <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>
+                        <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option>
                         <option value="logreg">Logistic regression</option>
                     </param>
                     <when value="t-test">