Mercurial > repos > sanbi-uwc > data_manager_primer_scheme_bedfiles
changeset 8:730e8bf0763d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit ec88f278d061a0ed14b92e0563d276a30fb04b71-dirty"
| author | sanbi-uwc |
|---|---|
| date | Wed, 22 Apr 2020 08:52:45 +0000 |
| parents | e5552d150daf |
| children | ca4eaf095d5d |
| files | data_manager/install_primer_scheme_bedfiles.py data_manager/install_primer_scheme_bedfiles.xml tool-data/primer_scheme_bedfiles.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/install_primer_scheme_bedfiles.py Sat Apr 18 16:37:22 2020 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.py Wed Apr 22 08:52:45 2020 +0000 @@ -17,9 +17,9 @@ def fetch_artic_primers(output_directory, primers): primer_sets = { - "ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed", - "ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed", - "ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed", + "SARS-CoV-2-ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed", + "SARS-CoV-2-ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed", + "SARS-CoV-2-ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed", } data = []
--- a/data_manager/install_primer_scheme_bedfiles.xml Sat Apr 18 16:37:22 2020 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.xml Wed Apr 22 08:52:45 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.8" tool_type="manage_data" profile="19.05"> +<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.9" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package">python</requirement> <requirement type="package" version="2.22.0">requests</requirement> @@ -61,4 +61,4 @@ </output> </test> </tests> -</tool> \ No newline at end of file +</tool>
--- a/tool-data/primer_scheme_bedfiles.loc.sample Sat Apr 18 16:37:22 2020 +0000 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Wed Apr 22 08:52:45 2020 +0000 @@ -5,4 +5,4 @@ # value description path # # for example -# ARTICv1 ARTIC v1 primers /data/galaxy/tool_data/artic_primers/ARTICv1.bed \ No newline at end of file +# SARS-CoV-2-ARTICv1 SARS-CoV-2 ARTIC v1 primers /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
--- a/tool_data_table_conf.xml.sample Sat Apr 18 16:37:22 2020 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 08:52:45 2020 +0000 @@ -1,6 +1,6 @@ <tables> <!-- Locations of primer scheme BED files --> - <table name="primer_scheme_bedfiles" comment_char="#"> + <table name="primer_scheme_bedfiles" comment_char="#" allow_duplicate_entries="False"> <columns>value, description, path</columns> <file path="tool-data/primer_scheme_bedfiles.loc" /> </table>