| Previous changeset 0:ae730ecdc7e7 (2020-04-19) Next changeset 2:b3710e492ee4 (2020-06-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6" |
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modified:
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 |
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| diff -r ae730ecdc7e7 -r cce5d9327cd6 data_manager/install_primer_scheme_bedfiles.py --- a/data_manager/install_primer_scheme_bedfiles.py Sun Apr 19 09:22:19 2020 -0400 +++ b/data_manager/install_primer_scheme_bedfiles.py Fri Apr 24 16:10:30 2020 -0400 |
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| @@ -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 = [] |
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| diff -r ae730ecdc7e7 -r cce5d9327cd6 data_manager/install_primer_scheme_bedfiles.xml --- a/data_manager/install_primer_scheme_bedfiles.xml Sun Apr 19 09:22:19 2020 -0400 +++ b/data_manager/install_primer_scheme_bedfiles.xml Fri Apr 24 16:10:30 2020 -0400 |
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| @@ -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="0.0.10" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package">python</requirement> <requirement type="package" version="2.22.0">requests</requirement> @@ -23,9 +23,9 @@ </param> <when value="ARTIC"> <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> - <option value="ARTICv1" selected="true">ARTIC v1</option> - <option value="ARTICv2" selected="true">ARTIC v2</option> - <option value="ARTICv3" selected="true">ARTIC v3</option> + <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option> + <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option> + <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option> </param> </when> <when value="history"> @@ -42,7 +42,7 @@ <tests> <test> <param name="input_type" value="ARTIC" /> - <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/> + <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/> <output name="output_file"> <assert_contents> <has_text text="ARTIC"/> @@ -61,4 +61,4 @@ </output> </test> </tests> -</tool> \ No newline at end of file +</tool> |
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| diff -r ae730ecdc7e7 -r cce5d9327cd6 tool-data/primer_scheme_bedfiles.loc.sample --- a/tool-data/primer_scheme_bedfiles.loc.sample Sun Apr 19 09:22:19 2020 -0400 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Fri Apr 24 16:10:30 2020 -0400 |
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| @@ -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 |
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| diff -r ae730ecdc7e7 -r cce5d9327cd6 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Apr 19 09:22:19 2020 -0400 +++ b/tool_data_table_conf.xml.sample Fri Apr 24 16:10:30 2020 -0400 |
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| @@ -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> |