0.4.0

Implemented enhancements:

• Dropping unnecessary columns #21
• Adding support for all official ENA checklists #20
• Possibility to give the taxon_id through the table #6

Closed issues:

• Library name generation #23

Merged pull requests:

• Taxon ID parsing improvements #27 (bedroesb)
• Adding support for all official sample checklists on ENA #26 (bedroesb)
• Taking away the need to give columns that are automatically filled in by the tool #25 (bedroesb)
• Allow to skip file upload and provide a file of filenames as source for data files #24 (mobilegenome)
• Adding support for multiple checklists #19 (bedroesb)
• Read md5sum from table, and only generate if missing #18 (mobilegenome)
• Add ENA_template_ERC000011_sample.xml #17 (rabuono)
• Small fixes based on #15 #16 (bedroesb)

NOTE: This release is not backwards compatible with previous release! Check following things if you update from 0.3.1 or earlier:

• Headers in the sample table will now follow the exact vocabulary as on ENA
• The --vir parameter is not supported anymore and is replaced by --checklist ERC000033 + support for all official checklists
• The scientific_name column in the sample table is not mandatory anymore + the taxon_id column is recommended instead
• Sample columns accession,submission_date, status are not needed anymore

0.3.1

• Support for all optional and recommended fields for viral submissions based on the ERC000033 checklist
• Support for empty values in optional and recommended fields (these will not be included in the final XML)

0.3.0

This release includes:

• Updated the XSD templates from ENA enabling correct local validations of the tables
• Updated XML templates to support new fields
• Replacing the curl dependency with the requests library from python (thank you @mobilegenome!)
• --version option to print out the version of the tool

0.2.8

• Support for non mandatory columns in the viral sample table (Thanks @tpall !)

0.2.7

• Better parsing of accession numbers and outputted in stdout in a tab separated manner
• Receipt is outputted as a receipt.xml file in the working directory
• Better handling of errors that do not produce a receipt
• Dropping support for python v2.X

Zenodo release

0.2.6

add usegalaxy.eu badge

0.2.5

• --tool option split in two: --tool TOOL_NAME default='ena-upload-cli' and --tool_version TOOL_VERSION default='0.2.5'
• --tool is not a mandatory option anymore
• tool_name and tool_version used for extra metadata fields in run, experiment, study and sample tables:

        <RUN_ATTRIBUTES>
            <RUN_ATTRIBUTE>
                <TAG>SUBMISSION_TOOL</TAG>
                <VALUE>${tool_name}</VALUE>
            </RUN_ATTRIBUTE>
            <RUN_ATTRIBUTE>
                <TAG>SUBMISSION_TOOL_VERSION</TAG>
                <VALUE>${tool_version}</VALUE>
            </RUN_ATTRIBUTE>
        </RUN_ATTRIBUTES>

0.2.4

• no support for password and webin-id as argument foor the tool anymore
• credentials are passed through .secret.yml file

0.2.3

• better password parsing from .secret file

0.2.2

• SUBMISSION_TOOL tag added to all templates