# HG changeset patch
# User iuc
# Date 1724147305 0
# Node ID e299752da98ea42cd5384d0746588d52822f19c5
# Parent  d600e09474687b9c4f58da28c55f7af74f079d0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0

diff -r d600e0947468 -r e299752da98e filter.xml
--- a/filter.xml	Wed Jul 31 18:06:35 2024 +0000
+++ b/filter.xml	Tue Aug 20 09:48:25 2024 +0000
@@ -524,7 +524,7 @@
                     <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad">
+            <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad" ftype="h5ad">
                 <assert_contents>
                     <has_h5_keys keys="obs, var, uns" />
                 </assert_contents>
diff -r d600e0947468 -r e299752da98e macros.xml
--- a/macros.xml	Wed Jul 31 18:06:35 2024 +0000
+++ b/macros.xml	Tue Aug 20 09:48:25 2024 +0000
@@ -435,6 +435,10 @@
             </when>
             <when value="customfile">
                 <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
+                <param name="header" type="select" label="Header in the list of markers?">
+                    <option value="included">Header incldued</option>
+                    <option value="not_included">Header not included</option>
+                </param>
             </when>
         </conditional>
     </xml>
@@ -471,6 +475,12 @@
         <expand macro="param_groupby"/>
         <expand macro="param_num_categories"/>
     </xml>
+    <token name="@CMD_var_names_header_check@"><![CDATA[
+header='infer'
+#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
+header=None
+#end if
+    ]]></token>
     <token name="@CMD_params_inputs@"><![CDATA[
     #if $method.var_names.type == 'custom'
     #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
diff -r d600e0947468 -r e299752da98e test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad
Binary file test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad has changed
diff -r d600e0947468 -r e299752da98e test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad
Binary file test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad has changed
diff -r d600e0947468 -r e299752da98e test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png
Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png has changed
diff -r d600e0947468 -r e299752da98e test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png
Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png has changed