diff cluster_reduce_dimension.xml @ 12:6acb08931836 draft

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

--- a/cluster_reduce_dimension.xml	Wed Nov 08 14:46:29 2023 +0000
+++ b/cluster_reduce_dimension.xml	Fri Nov 17 09:13:40 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description>with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -110,7 +110,7 @@
 #else if $method.method == 'tl.tsne'
 sc.tl.tsne(
     adata=adata,
-    #if $method.n_pcs
+    #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
     perplexity=$method.perplexity,
@@ -126,7 +126,7 @@
     min_dist=$method.min_dist,
     spread=$method.spread,
     n_components=$method.n_components,
-    #if $method.maxiter
+    #if str($method.maxiter) != ''
     maxiter=$method.maxiter,
     #end if
     alpha=$method.alpha,
@@ -137,7 +137,6 @@
     copy=False)
 
 #else if $method.method == 'tl.draw_graph'
-
     #if str($method.adjacency) != 'None'
 from scipy import io
 adjacency = io.mmread('$method.adjacency')
@@ -146,18 +145,18 @@
 sc.tl.draw_graph(
     adata=adata,
     layout='$method.layout',
-#if str($method.root) != ''
+#if $method.root
     #set $root=([int(x.strip()) for x in str($method.root).split(',')])
     root=$root,
 #end if
     random_state=$method.random_state,
-    #if str($method.init_pos) != ''
+    #if $method.init_pos
     init_pos='$method.init_pos',
     #end if
     #if str($method.adjacency) != 'None'
     adjacency=adjacency,
     #end if
-    #if str($method.key_ext) != ''
+    #if $method.key_ext
     key_ext='$method.key_ext',
     #end if
     copy=False)
@@ -183,10 +182,10 @@
 sc.tl.embedding_density(
     adata=adata,
     basis='$method.basis',
-#if str($method.groupby) != ''
+#if $method.groupby
     groupby='$method.groupby',
 #end if
-#if str($method.key_added) != ''
+#if $method.key_added
     key_added='$method.key_added',
 #end if
     )