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(-) [+]
line wrap: on
line diff
--- 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	${__HERE__}/sars-cov-2/SARS-CoV-2-ARTICv1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed	Wed Apr 22 06:06:22 2020 -0400
@@ -0,0 +1,196 @@
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Binary file test-data/sars-cov-2/sars_cov2_trimmed.bam has changed
Binary file test-data/sars-cov-2/sars_cov2_untrimmed.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/primer_scheme_bedfiles.loc.sample	Wed Apr 22 06:06:22 2020 -0400
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of primer schemes used for amplicon
+# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol)
+#
+# the columns are:
+# value  description path
+#
+# for example
+# SARS-CoV-2-ARTICv1   SARS-CoV-2-ARTIC v1 primers    /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Apr 22 06:06:22 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of primer scheme BED files -->
+    <table name="primer_scheme_bedfiles" comment_char="#">
+        <columns>value, description, path</columns>
+        <file path="tool-data/primer_scheme_bedfiles.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Apr 22 06:06:22 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of primer scheme BED files -->
+    <table name="primer_scheme_bedfiles" comment_char="#">
+        <columns>value, description, path</columns>
+        <file path="${__HERE__}/test-data/primer_scheme_bedfiles.loc" />
+    </table>
+</tables>