analysis_RefAlignment.xml

<?xml version='1.0' encoding='UTF-8'?>
<ANALYSIS_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.analysis.xsd">
  <ANALYSIS alias="TODO: Submitter designated name for the 'Analysis'. The name must be unique within the submission account." center_name="TODO: The center name (its acronym) of the submitter's account" broker_name="TODO: The center name (its acronym) of the broker" analysis_date="TODO: ISO date when the Analysis took place (e.g. '2001-12-17T09:30:47Z'). If the time stamp is unknown, leave it as 0s (2008-07-02T00:00:00)" analysis_center="TODO: If applicable, the name of the center that executed the Analysis.">
    <TITLE>TODO: Short text describing the Analysis. It will be displayed in search results.</TITLE>    <!-- Optional block -->
    <DESCRIPTION>TODO: Describes the analysis in detail</DESCRIPTION>   <!-- Optional block -->
    <STUDY_REF refname="TODO: Alias of the parent study, used to identify it."/>   <!-- Optional block -->
    <SAMPLE_REF refname="TODO: The alias of a sample associated with the analysis." label="TODO: A label associating the sample with sample references in data files."/>    <!-- Optional block -->
    <!-- If you want to provide several references to submitted samples, repeat <SAMPLE_REF> here as many times as needed. -->
    <EXPERIMENT_REF refname="TODO: The alias of an Experiment associated with the analysis"/>    <!-- Optional block -->
    <!-- If you want to provide several references to submitted experiments, repeat <EXPERIMENT_REF> here as many times as needed. -->
    <RUN_REF refname="TODO: The alias of a Run associated with the analysis." label="TODO: A label associating the run with run references in data files"/>    <!-- Optional block -->
    <!-- If you want to provide several references to submitted runs, repeat <RUN_REF> here as many times as needed. -->
    <ANALYSIS_REF refname="TODO: The alias of an Analysis associated with the analysis (i.e. the one you are submitting)." label="TODO: A label associating the analysis with analysis references in data files."/>    <!-- Optional block -->
    <!-- If you want to provide several references to other submitted analysis, repeat <ANALYSIS_REF> here as many times as needed. -->
    <ANALYSIS_TYPE>
      <REFERENCE_ALIGNMENT>
        <ASSEMBLY>    <!-- Optional block -->
          <STANDARD refname="TODO: Standard genome assembly name (e.g. GRCh37). Use this column exclusively if the Analysis is a Reference Alignment." accession="TODO: Standard genome accession version (e.g. GCA_000001405.1). Use this column exclusively if the Analysis is a Reference Alignment."/>
        </ASSEMBLY>
        <SEQUENCE accession="TODO: Accession of the sequence for the reference alignment in format 'Accession.version', with version being mandatory (e.g. CM000663.1). Use this column exclusively if the Analysis is a Reference Alignment or Sequence Variation." label="TODO:  This is how Reference Sequence is labeled in submission file(s) (e.g. chr1). It is equivalent to the @SQ label in a BAM file (optional when submitted file uses INSDC accession.version). Use this column exclusively if the Analysis is a Reference Alignment or Sequence Variation."/>   <!-- Optional block -->
        <!-- If you want to provide several reference sequences, repeat <SEQUENCE> here as many times as needed. -->
      </REFERENCE_ALIGNMENT>
    </ANALYSIS_TYPE>
    <FILES>
      <FILE filename="TODO: The name or relative pathname of an Analysis data file (e.g. path/to/files/file.fastq)" filetype= "TODO: The run data file type. Must be value from Controlled vocabulary: 'tab', 'bam', 'bai', 'cram', 'crai', 'vcf', 'vcf_aggregate', 'bcf', 'tabix', 'wig', 'bed', 'gff', 'fasta', 'fastq', 'flatfile', 'chromosome_list', 'sample_list', 'readme_file', 'phenotype_file', 'BioNano_native', 'Kallisto_native', 'agp', 'unlocalised_list', 'info', 'manifest', 'csi', 'bcf_aggregate', 'other'." checksum_method="MD5" checksum="TODO: CHECKSUM from encrypted file (e.g. 298ee70555532679d7c1f91b5dd07aef)" unencrypted_checksum="TODO: CHECKSUM from unencrypted file (e.g. e609bc52c035ff1a62cdba0f0689889j)" checklist="TODO: The name of the checklist."/>
      <!-- If you want to provide several files, repeat <FILE> here as many times as needed. -->
    </FILES>
    <ANALYSIS_ATTRIBUTES>   <!-- Optional block -->
      <ANALYSIS_ATTRIBUTE>
        <TAG>TODO: Name of the custom attribute.</TAG>
        <VALUE>TODO: Value of the custom attribute.</VALUE>
        <UNITS>TODO: Optional scientific units.</UNITS>
      </ANALYSIS_ATTRIBUTE>
      <!-- If you want to provide several custom analysis attributes, repeat <ANALYSIS_ATTRIBUTE> (with at least TAG and VALUE) here as many times as needed. -->
    </ANALYSIS_ATTRIBUTES>
  </ANALYSIS>
  <!--  If you are submitting more than one Analysis, replicate the block <ANALYSIS> here, 
          as many times as necessary.  -->
</ANALYSIS_SET>