Mercurial > repos > sanbi-uwc > vcf_to_alignment
changeset 1:4b9ddf64558d draft
planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit c467fa511c437e11ea72b912975d64631b8d0f98
| author | sanbi-uwc |
|---|---|
| date | Wed, 01 Feb 2017 07:07:32 -0500 |
| parents | cc255feec53b |
| children | a0c85f2d74a5 |
| files | tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample vcf_to_alignment.xml |
| diffstat | 3 files changed, 15 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Feb 01 07:07:32 2017 -0500 @@ -0,0 +1,7 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Feb 01 07:07:32 2017 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- a/vcf_to_alignment.xml Wed Feb 01 06:56:24 2017 -0500 +++ b/vcf_to_alignment.xml Wed Feb 01 07:07:32 2017 -0500 @@ -18,7 +18,7 @@ #if str($reference.source) == 'history': reference.fasta #else - '${reference.builtin}' + '${reference.builtin.fields.path}' #end if --output_file '${output_alignment}' ]]> @@ -36,6 +36,7 @@ <when value="builtin"> <param name="builtin" type="select" label="Reference sequence (FASTA format)"> <options from_data_table="all_fasta" /> + <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" /> </param> </when> </conditional>