# HG changeset patch
# User fubar
# Date 1718440453 0
# Node ID f132065ac1704a6166f5f015b18da1821166a77a
# Parent  78e7461e89469fd4ed08d2ebf8e472ecfc6ae4b7
planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/

diff -r 78e7461e8946 -r f132065ac170 bam_bed_gff_to_bigwig.xml
--- a/bam_bed_gff_to_bigwig.xml	Fri Jun 14 23:46:42 2024 +0000
+++ b/bam_bed_gff_to_bigwig.xml	Sat Jun 15 08:34:13 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="bbgtobigwig_dev" name="BAM BED GFF coverage bigWigs" version="0.1" profile="22.05"> 
+<tool id="bbgtobigwig" name="BAM BED GFF coverage bigWigs" version="0.1" profile="22.05"> 
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
     </xrefs>
@@ -96,7 +96,7 @@
 
    Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
  
-   A chromosome lengths file must be provided if the input has a missing dbkey='?' on the pencil (edit attributes) tab. 
+   A chromosome lengths file must be provided if the input has a missing dbkey (='?') on the pencil (edit attributes) form. 
    
    The actual reference is not needed. The Compute sequence length tool can generate the lengths file.
  
diff -r 78e7461e8946 -r f132065ac170 test-data/dbkeys.loc.sample
--- a/test-data/dbkeys.loc.sample	Fri Jun 14 23:46:42 2024 +0000
+++ b/test-data/dbkeys.loc.sample	Sat Jun 15 08:34:13 2024 +0000
@@ -1,1 +1,2 @@
 #<dbkey>	<display_name>	<len_file_path>
+hg38	hg38	testing.len
diff -r 78e7461e8946 -r f132065ac170 tool-data/dbkeys.loc.sample
--- a/tool-data/dbkeys.loc.sample	Fri Jun 14 23:46:42 2024 +0000
+++ b/tool-data/dbkeys.loc.sample	Sat Jun 15 08:34:13 2024 +0000
@@ -1,1 +1,2 @@
 #<dbkey>	<display_name>	<len_file_path>
+hg38	hg38	testing.len
diff -r 78e7461e8946 -r f132065ac170 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Jun 14 23:46:42 2024 +0000
+++ b/tool_data_table_conf.xml.sample	Sat Jun 15 08:34:13 2024 +0000
@@ -2,6 +2,7 @@
     <!-- Locations of dbkeys and len files under genome directory -->
     <table name="__dbkeys__" comment_char="#">
         <columns>value, name, len_path</columns>
-        <file path="test-data/dbkeys.loc" />
+        <file path="tool-data/dbkeys.loc" />
     </table>
 </tables>
+