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Merge pull request #39 from usegalaxy-eu/sample-fix
Adding back tool name to sample metadata
2 parents 4c5b464 + 08f8430 commit 6846801

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+328
-30
lines changed

‎ena_upload/templates/ENA_template_samples.xml

Lines changed: 8 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -6,14 +6,6 @@ def attributetest(row, column):
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return True
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else:
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return False
9-
{%- if 'mandatory' not in attributes.values() %}
10-
def onlyoptional(row):
11-
attributelist = {{ attributes.keys() | list }}
12-
for column in attributelist:
13-
if hasattr(row, column) and pd.notna(row[column]) and not row[column].isspace() and str(row[column]).lower() not in ['nan', 'na']:
14-
return True
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return False
16-
{%- endif %}
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?>
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<SAMPLE_SET xmlns:py="http://genshi.edgewall.org/"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
@@ -29,9 +21,6 @@ def onlyoptional(row):
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</py:if>
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</SAMPLE_NAME>
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<DESCRIPTION>${row.sample_description}</DESCRIPTION>
32-
{%- if 'mandatory' not in attributes.values() %}
33-
<py:if test="onlyoptional(row)">
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{%- endif %}
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<SAMPLE_ATTRIBUTES>
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{%- for key, value in attributes.items() %}
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{%- if value == 'mandatory' %}
@@ -48,10 +37,15 @@ def onlyoptional(row):
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</py:if>
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{%- endif %}
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{%- endfor %}
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
43+
</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
46+
<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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{%- if 'mandatory' not in attributes.values() %}
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</py:if>
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{%- endif %}
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</SAMPLE>
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</py:for>
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</SAMPLE_SET>

‎ena_upload/templates/ENA_template_samples_ERC000011.xml

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,6 @@ def attributetest(row, column):
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return True
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else:
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return False
9-
def onlyoptional(row):
10-
attributelist = ['cell_type', 'dev_stage', 'germline', 'tissue_lib', 'tissue_type', 'collection_date', 'isolation_source', 'lat_lon', 'collected_by', 'geographic location (country and/or sea)', 'geographic location (region and locality)', 'identified_by', 'environmental_sample', 'mating_type', 'sex', 'lab_host', 'host scientific name', 'bio_material', 'culture_collection', 'specimen_voucher', 'cultivar', 'ecotype', 'isolate', 'sub_species', 'variety', 'sub_strain', 'cell_line', 'serotype', 'serovar', 'strain']
11-
for column in attributelist:
12-
if hasattr(row, column) and pd.notna(row[column]) and not row[column].isspace() and str(row[column]).lower() not in ['nan', 'na']:
13-
return True
14-
return False
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?>
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<SAMPLE_SET xmlns:py="http://genshi.edgewall.org/"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
@@ -27,7 +21,6 @@ def onlyoptional(row):
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</py:if>
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</SAMPLE_NAME>
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<DESCRIPTION>${row.sample_description}</DESCRIPTION>
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<py:if test="onlyoptional(row)">
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<SAMPLE_ATTRIBUTES>
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<py:if test="attributetest(row, 'cell_type')">
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<SAMPLE_ATTRIBUTE>
@@ -209,8 +202,15 @@ def onlyoptional(row):
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<VALUE>${row['strain']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</py:if>
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</SAMPLE>
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</py:for>
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</SAMPLE_SET>

‎ena_upload/templates/ENA_template_samples_ERC000012.xml

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@@ -466,6 +466,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000013.xml

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@@ -552,6 +552,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000014.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000015.xml

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@@ -498,6 +498,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000016.xml

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@@ -492,6 +492,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000017.xml

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@@ -498,6 +498,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000018.xml

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@@ -540,6 +540,14 @@ def attributetest(row, column):
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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000019.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000020.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000021.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000022.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000023.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000024.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000025.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000027.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000028.xml

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<VALUE>${row['strain']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000029.xml

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@@ -278,6 +278,14 @@ def attributetest(row, column):
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<VALUE>${row['isolation source non-host-associated']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
282+
<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000030.xml

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<VALUE>${row['Further Details']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000031.xml

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<VALUE>${row['perturbation']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000032.xml

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<VALUE>${row['isolation source non-host-associated']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

‎ena_upload/templates/ENA_template_samples_ERC000033.xml

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<VALUE>${row['isolation source non-host-associated']}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</py:if>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL</TAG>
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<VALUE>${tool_name}</VALUE>
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</SAMPLE_ATTRIBUTE>
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<SAMPLE_ATTRIBUTE>
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<TAG>SUBMISSION_TOOL_VERSION</TAG>
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<VALUE>${tool_version}</VALUE>
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</SAMPLE_ATTRIBUTE>
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</SAMPLE_ATTRIBUTES>
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</SAMPLE>
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</py:for>

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