| Previous changeset 1:2b95d5c04908 (2020-04-04) Next changeset 3:2c47c138176e (2020-06-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc" |
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modified:
macros.xml |
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added:
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 |
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| diff -r 2b95d5c04908 -r f91cfb73d369 macros.xml --- a/macros.xml Sat Apr 04 12:37:00 2020 -0400 +++ b/macros.xml Wed Apr 22 06:06:56 2020 -0400 |
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| @@ -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> |
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| diff -r 2b95d5c04908 -r f91cfb73d369 test-data/primer_scheme_bedfiles.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Wed Apr 22 06:06:56 2020 -0400 |
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| @@ -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 |
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| diff -r 2b95d5c04908 -r f91cfb73d369 test-data/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 06:06:56 2020 -0400 |
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| b'@@ -0,0 +1,196 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| diff -r 2b95d5c04908 -r f91cfb73d369 test-data/sars-cov-2/sars_cov2_trimmed.bam |
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| Binary file test-data/sars-cov-2/sars_cov2_trimmed.bam has changed |
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| diff -r 2b95d5c04908 -r f91cfb73d369 test-data/sars-cov-2/sars_cov2_untrimmed.bam |
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| Binary file test-data/sars-cov-2/sars_cov2_untrimmed.bam has changed |
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| diff -r 2b95d5c04908 -r f91cfb73d369 tool-data/primer_scheme_bedfiles.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Wed Apr 22 06:06:56 2020 -0400 |
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| @@ -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 |
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| diff -r 2b95d5c04908 -r f91cfb73d369 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 06:06:56 2020 -0400 |
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| @@ -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> |
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| diff -r 2b95d5c04908 -r f91cfb73d369 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Apr 22 06:06:56 2020 -0400 |
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| @@ -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> |