Mercurial > repos > iuc > bwameth
changeset 1:404fae08ea31 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit f96ef202e742cc1d260bce023ae0d1e1499a11d8
| author | iuc |
|---|---|
| date | Wed, 21 Dec 2016 17:49:54 -0500 |
| parents | f7094efef903 |
| children | 2e4674c16615 |
| files | bwameth.xml tool-data/bwameth_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/bwameth.xml Wed Sep 14 16:55:47 2016 -0400 +++ b/bwameth.xml Wed Dec 21 17:49:54 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="bwameth" name="bwameth" version="0.2.0"> +<tool id="bwameth" name="bwameth" version="0.2.0.2"> <description>Fast and accurate aligner of BS-Seq reads.</description> <requirements> <requirement type="package" version="1.2">samtools</requirement> @@ -41,7 +41,7 @@ <option value="indexed">Use a built-in index</option> </param> <when value="history"> - <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" /> + <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" /> </when> <when value="indexed"> <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
--- a/tool-data/bwameth_indexes.loc.sample Wed Sep 14 16:55:47 2016 -0400 +++ b/tool-data/bwameth_indexes.loc.sample Wed Dec 21 17:49:54 2016 -0500 @@ -1,10 +1,15 @@ # This is a sample file distributed with Galaxy that is used to define a # list of bwa-meth indices, using three columns tab separated: # -# bwameth_index_id\tSome description text\t/path/to/genome.fasta +# <unique_build_id> <dbkey> <display_name> <genome_fasta_file_path> # # An index can be created with the following command: # # bwameth.py index /some/path/genome.fa # # "/some/path/genome.fa" would then be the last column in the line +# If this were for the mm10 mouse genome, the resulting entry would look like: +# +#mm9 mm9 Mouse (mm9) /some/path/genome.fa +# +#
--- a/tool_data_table_conf.xml.sample Wed Sep 14 16:55:47 2016 -0400 +++ b/tool_data_table_conf.xml.sample Wed Dec 21 17:49:54 2016 -0500 @@ -1,6 +1,6 @@ <tables> - <table name="bwameth_indexes" comment_char="#"> - <columns>value, name, path</columns> + <table name="bwameth_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> <file path="tool-data/bwameth_indexes.loc" /> </table> </tables>