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-rw-r--r--bh20simplewebuploader/templates/ebi-sample.xml43
1 files changed, 13 insertions, 30 deletions
diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml
index 694c471..441e29e 100644
--- a/bh20simplewebuploader/templates/ebi-sample.xml
+++ b/bh20simplewebuploader/templates/ebi-sample.xml
@@ -1,62 +1,46 @@
<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
- <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
- <TITLE>human gastric microbiota, mucosal</TITLE>
+ <SAMPLE alias="{{ id }}" center_name="COVID-19 PubSeq">
+ <TITLE>COVID-19 PubSeq Sample</TITLE>
<SAMPLE_NAME>
- <TAXON_ID>1284369</TAXON_ID>
- <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
- <COMMON_NAME></COMMON_NAME>
+ <TAXON_ID>2697049</TAXON_ID>
+ <SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME>
+ <COMMON_NAME>SARS-CoV-2</COMMON_NAME>
</SAMPLE_NAME>
<SAMPLE_ATTRIBUTES>
<SAMPLE_ATTRIBUTE>
<TAG>investigation type</TAG>
- <VALUE>mimarks-survey</VALUE>
+ <VALUE>{{ investigation_type }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sequencing method</TAG>
- <VALUE>pyrosequencing</VALUE>
+ <VALUE>{{ sequence_method }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>collection date</TAG>
- <VALUE>2010</VALUE>
- </SAMPLE_ATTRIBUTE>
- <SAMPLE_ATTRIBUTE>
- <TAG>host body site</TAG>
- <VALUE>Mucosa of stomach</VALUE>
- </SAMPLE_ATTRIBUTE>
- <SAMPLE_ATTRIBUTE>
- <TAG>human-associated environmental package</TAG>
- <VALUE>human-associated</VALUE>
+ <VALUE>{{ time }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (latitude)</TAG>
- <VALUE>1.81</VALUE>
+ <VALUE>{{ latidude }}</VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (longitude)</TAG>
- <VALUE>-78.76</VALUE>
+ <VALUE>{{ longitude }}</VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (country and/or sea)</TAG>
- <VALUE>Colombia</VALUE>
+ <VALUE>{{ country }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (region and locality)</TAG>
- <VALUE>Tumaco</VALUE>
- </SAMPLE_ATTRIBUTE>
- <SAMPLE_ATTRIBUTE>
- <TAG>environment (biome)</TAG>
- <VALUE>coast</VALUE>
- </SAMPLE_ATTRIBUTE>
- <SAMPLE_ATTRIBUTE>
- <TAG>environment (feature)</TAG>
- <VALUE>human-associated habitat</VALUE>
+ <VALUE>{{ locality }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>environment (material)</TAG>
- <VALUE>gastric biopsy</VALUE>
+ <VALUE>{{ material }}</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>ENA-CHECKLIST</TAG>
@@ -65,4 +49,3 @@
</SAMPLE_ATTRIBUTES>
</SAMPLE>
</SAMPLE_SET>
-