htsworkflow/templates/geo_submission.soft

   1 {% for name, value in series %}{{name}} = {{value}}
   2 {% endfor %}!Series_platform_id = {{ platform_id }}
   3 {% for row in samples %}
   4 ^SAMPLE={{row.name}}
   5 !Sample_type=SRA
   6 !Sample_title={{row.name}}
   7 !Sample_series_id = {{ series_id }}
   8 !Sample_instrument_model = Illumina Genome Analyzer
   9 !Sample_instrument_model = Illumina Genome Analyzer II
  10 !Sample_instrument_model = Illumina Genome Analyzer IIx
  11 !Sample_instrument_model = Illumina HiSeq 2000
  12 !Sample_channel_count = 1
  13 !Sample_organism_ch1 = {{ row.species_name }}
  14 !Sample_taxid_ch1 = {{ row.taxon_id }}
  15 !Sample_platform_id = {{ platform_id }}
  16 !Sample_source_name_ch1={{row.cell}}
  17 !Sample_library_strategy={{ row.experiment_type }}
  18 !Sample_library_source={{row.library_source}}
  19 !Sample_library_selection={{ row.library_selection }}
  20 !Sample_growth_protocol_ch1={{ row.growthProtocol|safe }}
  21 !Sample_extract_protocol={{ row.extractProtocol|safe }}
  22 !Sample_data_processing={{ row.dataProtocol|safe }}
  23 !Sample_molecule_ch1 = {{ row.extractMolecule }}
  24 !Sample_characteristics_ch1 = labExpId: {{ row.library_id }}
  25 !Sample_characteristics_ch1 = replicate: {{ row.replicate }}
  26 {% if row.cell %}{% spaceless %}
  27 !Sample_characteristics_ch1 = cell: {{ row.cell }}
  28 {% endspaceless %}{% endif %}
  29 {% if row.readType %}{% spaceless %}
  30 !Sample_characteristics_ch1 = readType: {{ row.readType }}
  31 {% endspaceless %}{% endif %}{% if row.antibody %}{% spaceless %}
  32 !Sample_characteristics_ch1 = cell: {{ row.antibody }}
  33 {% endspaceless %}{% endif %}{% for raw in row.raw %}
  34 !Sample_raw_file_{{forloop.counter}}={{raw.filename}}
  35 !Sample_raw_file_type_{{forloop.counter}}={{raw.file_type_label}}
  36 !Sample_raw_file_checksum_{{forloop.counter}}={{raw.md5sum}}{% endfor %}{% for sup in row.supplimental %}
  37 !Sample_supplementary_file_{{forloop.counter}}={{sup.filename}}
  38 !Sample_supplementary_file_checksum_{{forloop.counter}}={{sup.md5sum}}
  39 {% endfor %}{% endfor %}