Mercurial > repos > fubar > bbgbigwig_dev
changeset 5:f132065ac170 draft
planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
| author | fubar |
|---|---|
| date | Sat, 15 Jun 2024 08:34:13 +0000 |
| parents | 78e7461e8946 |
| children | 4043d4155909 |
| files | bam_bed_gff_to_bigwig.xml test-data/dbkeys.loc.sample tool-data/dbkeys.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- 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.
--- 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
--- 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
--- 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> +