Merge pull request #105 from usegalaxy-eu/checklist_update

Automatic update of ENA Sample Checklists
usegalaxy-eu · Jan 27, 2025 · 5db67a8 · 5db67a8
2 parents 4ffbd0d + b38a418
commit 5db67a8
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diff --git a/ena_upload/templates/ENA_template_PLATFORM.xml b/ena_upload/templates/ENA_template_PLATFORM.xml
@@ -26,6 +26,7 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina miseq'">Illumina MiSeq</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina miniseq'">Illumina MiniSeq</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq x'">Illumina NovaSeq X</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq x plus'">Illumina NovaSeq X Plus</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq 6000'">Illumina NovaSeq 6000</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'nextseq 500'">NextSeq 500</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'nextseq 550'">NextSeq 550</INSTRUMENT_MODEL>
@@ -101,6 +102,7 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g400'">DNBSEQ-G400</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g50'">DNBSEQ-G50</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g400 fast'">DNBSEQ-G400 FAST</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-t10x4rs'">DNBSEQ-T10x4RS</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
 </DNBSEQ>
 <ELEMENT py:when="row.platform.lower().strip() == 'element'" py:choose="">

diff --git a/ena_upload/templates/ENA_template_samples_ERC000011.xml b/ena_upload/templates/ENA_template_samples_ERC000011.xml
@@ -87,12 +87,6 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['collection date']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'geographic location (region and locality)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (region and locality)</TAG>
@@ -123,6 +117,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sex']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'lab_host')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>lab_host</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000012.xml b/ena_upload/templates/ENA_template_samples_ERC000012.xml
@@ -179,12 +179,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -262,6 +256,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000013.xml b/ena_upload/templates/ENA_template_samples_ERC000013.xml
@@ -203,12 +203,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -285,6 +279,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000014.xml b/ena_upload/templates/ENA_template_samples_ERC000014.xml
@@ -203,12 +203,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -273,6 +267,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'nose/mouth/teeth/throat disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>nose/mouth/teeth/throat disorder</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000015.xml b/ena_upload/templates/ENA_template_samples_ERC000015.xml
@@ -191,12 +191,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -261,6 +255,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'gastrointestinal tract disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>gastrointestinal tract disorder</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000016.xml b/ena_upload/templates/ENA_template_samples_ERC000016.xml
@@ -197,12 +197,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -267,6 +261,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'nose/mouth/teeth/throat disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>nose/mouth/teeth/throat disorder</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000017.xml b/ena_upload/templates/ENA_template_samples_ERC000017.xml
@@ -191,12 +191,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -261,6 +255,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'dermatology disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>dermatology disorder</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000018.xml b/ena_upload/templates/ENA_template_samples_ERC000018.xml
@@ -191,12 +191,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -261,6 +255,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'gynecological disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>gynecological disorder</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000019.xml b/ena_upload/templates/ENA_template_samples_ERC000019.xml
@@ -179,12 +179,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -256,6 +250,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000020.xml b/ena_upload/templates/ENA_template_samples_ERC000020.xml
@@ -203,12 +203,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -297,6 +291,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000021.xml b/ena_upload/templates/ENA_template_samples_ERC000021.xml
@@ -198,12 +198,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -275,6 +269,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000022.xml b/ena_upload/templates/ENA_template_samples_ERC000022.xml
@@ -216,12 +216,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -317,6 +311,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['extreme_unusual_properties/Al saturation method']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000023.xml b/ena_upload/templates/ENA_template_samples_ERC000023.xml
@@ -179,12 +179,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -249,6 +243,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'biochemical oxygen demand')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>biochemical oxygen demand</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000024.xml b/ena_upload/templates/ENA_template_samples_ERC000024.xml
@@ -200,12 +200,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -277,6 +271,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>