Mercurial > repos > iuc > ivar_getmasked
changeset 2:d7e79eb3bcb3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
| author | iuc |
|---|---|
| date | Wed, 22 Apr 2020 06:06:22 -0400 |
| parents | ad0dc9f4c9e2 |
| children | 2cf4a1cafc16 |
| files | macros.xml test-data/primer_scheme_bedfiles.loc test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed test-data/sars-cov-2/sars_cov2_trimmed.bam test-data/sars-cov-2/sars_cov2_untrimmed.bam tool-data/primer_scheme_bedfiles.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 227 insertions(+), 1 deletions(-) [+] |
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--- a/macros.xml Sat Apr 04 12:34:02 2020 -0400 +++ b/macros.xml Wed Apr 22 06:06:22 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">1.2</token> + <token name="@VERSION@">1.2.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ivar</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Wed Apr 22 06:06:22 2020 -0400 @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of primer schemes used for amplicon +# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol) +# +# the columns are: +# value description path +# +# for example +SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 ${__HERE__}/sars-cov-2/SARS-CoV-2-ARTICv1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed Wed Apr 22 06:06:22 2020 -0400 @@ -0,0 +1,196 @@ +MN908947.3 30 54 nCoV-2019_1_LEFT 60 + +MN908947.3 385 410 nCoV-2019_1_RIGHT 60 - +MN908947.3 320 342 nCoV-2019_2_LEFT 60 + +MN908947.3 704 726 nCoV-2019_2_RIGHT 60 - +MN908947.3 642 664 nCoV-2019_3_LEFT 60 + +MN908947.3 1004 1028 nCoV-2019_3_RIGHT 60 - +MN908947.3 943 965 nCoV-2019_4_LEFT 60 + +MN908947.3 1312 1337 nCoV-2019_4_RIGHT 60 - +MN908947.3 1242 1264 nCoV-2019_5_LEFT 60 + +MN908947.3 1623 1651 nCoV-2019_5_RIGHT 60 - +MN908947.3 1573 1595 nCoV-2019_6_LEFT 60 + +MN908947.3 1942 1964 nCoV-2019_6_RIGHT 60 - +MN908947.3 1875 1897 nCoV-2019_7_LEFT 60 + +MN908947.3 2247 2269 nCoV-2019_7_RIGHT 60 - +MN908947.3 2181 2205 nCoV-2019_8_LEFT 60 + +MN908947.3 2568 2592 nCoV-2019_8_RIGHT 60 - +MN908947.3 2505 2529 nCoV-2019_9_LEFT 60 + +MN908947.3 2882 2904 nCoV-2019_9_RIGHT 60 - +MN908947.3 2826 2850 nCoV-2019_10_LEFT 60 + +MN908947.3 3183 3210 nCoV-2019_10_RIGHT 60 - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Wed Apr 22 06:06:22 2020 -0400 @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of primer schemes used for amplicon +# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol) +# +# the columns are: +# value description path +# +# for example +# SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 primers /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 06:06:22 2020 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of primer scheme BED files --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, description, path</columns> + <file path="tool-data/primer_scheme_bedfiles.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Apr 22 06:06:22 2020 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of primer scheme BED files --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, description, path</columns> + <file path="${__HERE__}/test-data/primer_scheme_bedfiles.loc" /> + </table> +</tables>