aboutsummaryrefslogtreecommitdiff
path: root/scripts/submit_ebi
diff options
context:
space:
mode:
Diffstat (limited to 'scripts/submit_ebi')
-rw-r--r--scripts/submit_ebi/example/project-submission.xml3
-rw-r--r--scripts/submit_ebi/example/project.xml3
-rw-r--r--scripts/submit_ebi/example/sample-submission.xml8
-rw-r--r--scripts/submit_ebi/example/sample.xml68
4 files changed, 80 insertions, 2 deletions
diff --git a/scripts/submit_ebi/example/project-submission.xml b/scripts/submit_ebi/example/project-submission.xml
index 2d3ddc1..1abb827 100644
--- a/scripts/submit_ebi/example/project-submission.xml
+++ b/scripts/submit_ebi/example/project-submission.xml
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
<SUBMISSION>
<ACTIONS>
<ACTION>
@@ -6,6 +7,6 @@
<ACTION>
<HOLD HoldUntilDate="2020-10-10"/>
</ACTION>
- </ACTIONS>
+ </ACTIONS>
</SUBMISSION>
diff --git a/scripts/submit_ebi/example/project.xml b/scripts/submit_ebi/example/project.xml
index 90704ab..6a817e7 100644
--- a/scripts/submit_ebi/example/project.xml
+++ b/scripts/submit_ebi/example/project.xml
@@ -1,7 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
<PROJECT_SET>
<PROJECT alias="PubSeq01">
<TITLE>Testing PubSeq Sample uploads</TITLE>
- <DESCRIPTION>This study aimed to allow for uploading sequences from PubSeq</DESCRIPTION>
+ <DESCRIPTION>This is a test to allow for uploading sequences from PubSeq</DESCRIPTION>
<SUBMISSION_PROJECT>
<SEQUENCING_PROJECT/>
</SUBMISSION_PROJECT>
diff --git a/scripts/submit_ebi/example/sample-submission.xml b/scripts/submit_ebi/example/sample-submission.xml
new file mode 100644
index 0000000..9d13512
--- /dev/null
+++ b/scripts/submit_ebi/example/sample-submission.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SUBMISSION>
+ <ACTIONS>
+ <ACTION>
+ <ADD/>
+ </ACTION>
+ </ACTIONS>
+</SUBMISSION>
diff --git a/scripts/submit_ebi/example/sample.xml b/scripts/submit_ebi/example/sample.xml
new file mode 100644
index 0000000..694c471
--- /dev/null
+++ b/scripts/submit_ebi/example/sample.xml
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SAMPLE_SET>
+ <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
+ <TITLE>human gastric microbiota, mucosal</TITLE>
+ <SAMPLE_NAME>
+ <TAXON_ID>1284369</TAXON_ID>
+ <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
+ <COMMON_NAME></COMMON_NAME>
+ </SAMPLE_NAME>
+ <SAMPLE_ATTRIBUTES>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>investigation type</TAG>
+ <VALUE>mimarks-survey</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>sequencing method</TAG>
+ <VALUE>pyrosequencing</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>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (latitude)</TAG>
+ <VALUE>1.81</VALUE>
+ <UNITS>DD</UNITS>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (longitude)</TAG>
+ <VALUE>-78.76</VALUE>
+ <UNITS>DD</UNITS>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>geographic location (country and/or sea)</TAG>
+ <VALUE>Colombia</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>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>environment (material)</TAG>
+ <VALUE>gastric biopsy</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ <SAMPLE_ATTRIBUTE>
+ <TAG>ENA-CHECKLIST</TAG>
+ <VALUE>ERC000011</VALUE>
+ </SAMPLE_ATTRIBUTE>
+ </SAMPLE_ATTRIBUTES>
+ </SAMPLE>
+</SAMPLE_SET>
+