changeset 20:62acdd96d4a0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9

--- a/macros.xml	Thu Oct 03 22:44:36 2024 +0000
+++ b/macros.xml	Fri Oct 18 10:37:11 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
@@ -1289,8 +1289,8 @@
     ]]>
     </token>
 
-    <xml name="param_gene_symbols">
-        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols" help="By default 'var_names' refer to the index column of the '.var' DataFrame">
+    <xml name="param_gene_symbols" token_label="Key for field in '.var' that stores gene symbols" token_help="By default 'var_names' refer to the index column of the '.var' DataFrame">
+        <param argument="gene_symbols" type="text" value="" optional="true" label="@LABEL@" help="@HELP@">
             <expand macro="sanitize_query"/>
         </param>
     </xml>

--- a/plot.xml	Thu Oct 03 22:44:36 2024 +0000
+++ b/plot.xml	Fri Oct 18 10:37:11 2024 +0000
@@ -223,6 +223,7 @@
 sc.pl.pca(
     @CMD_PARAM_PLOT_INPUTS@
     @CMD_PARAM_COLOR@
+    @CMD_PARAM_GENE_SYMBOLS@
     use_raw=$method.use_raw,
     sort_order=$method.sort_order,
     @CMD_PARAM_GROUPS@
@@ -282,6 +283,7 @@
 sc.pl.umap(
     @CMD_PARAM_PLOT_INPUTS@
     @CMD_PARAM_COLOR@
+    @CMD_PARAM_GENE_SYMBOLS@
     use_raw=$method.use_raw,
     @CMD_PL_EDGES@
     arrows=$method.arrows,
@@ -297,6 +299,7 @@
 sc.pl.diffmap(
     @CMD_PARAM_PLOT_INPUTS@
     @CMD_PARAM_COLOR@
+    @CMD_PARAM_GENE_SYMBOLS@
     use_raw=$method.use_raw,
     sort_order=$method.sort_order,
     @CMD_PARAM_GROUPS@
@@ -741,6 +744,7 @@
             </when>
             <when value="pl.pca">
                 <expand macro="param_color"/>
+                <expand macro="param_gene_symbols"/>
                 <expand macro="param_use_raw"/>
                 <expand macro="param_sort_order"/>
                 <expand macro="param_groups"/>
@@ -784,6 +788,7 @@
             </when>
             <when value="pl.umap">
                 <expand macro="param_color"/>
+                <expand macro="param_gene_symbols"/>
                 <expand macro="param_use_raw"/>
                 <expand macro="pl_edges"/>
                 <expand macro="param_arrows"/>
@@ -796,6 +801,7 @@
             </when>
             <when value="pl.diffmap">
                 <expand macro="param_color"/>
+                <expand macro="param_gene_symbols"/>
                 <expand macro="param_use_raw"/>
                 <expand macro="param_sort_order"/>
                 <expand macro="param_groups"/>
@@ -1602,6 +1608,7 @@
             <conditional name="method">
                 <param name="method" value="pl.pca"/>
                 <param name="color" value="CD3D,CD79A"/>
+                <param name="gene_symbols" value="symbol"/>
                 <section name="plot">
                     <repeat name="components">
                         <param name="axis1" value="1"/>
@@ -1637,6 +1644,7 @@
                     <has_text_matching expression="ncols=2"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
+                    <has_text_matching expression="gene_symbols='symbol'"/>
                 </assert_contents>
             </output>
             <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
@@ -1758,6 +1766,7 @@
             <conditional name="method">
                 <param name="method" value="pl.umap"/>
                 <param name="color" value="paul15_clusters"/>
+                <param name="gene_symbols" value="symbol"/>
                 <conditional name="edges">
                     <param name="edges" value="True"/>
                 </conditional>
@@ -1788,7 +1797,7 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-
+                    <has_text_matching expression="gene_symbols='symbol'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
@@ -1801,6 +1810,7 @@
             <conditional name="method">
                 <param name="method" value="pl.diffmap"/>
                 <param name="color" value="paul15_clusters"/>
+                <param name="gene_symbols" value="symbol"/>
                 <section name="plot">
                     <param name="legend_fontsize" value="1"/>
                     <param name="legend_fontweight" value="normal"/>
@@ -1825,7 +1835,7 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-
+                    <has_text_matching expression="gene_symbols='symbol'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>