interactivetool_ena_upload_template_builder.xml

<tool id="interactive_tool_ena_upload_templates" name="ENA upload template builder" version="0.1.0+galaxy0" profile="22.5">
<!-- <tool id="interactive_tool_ena_upload_templates" name="ENA upload template builder" tool_type="interactive" version="0.1.0+galaxy0" profile="22.5"> -->
    <description>create tables for the ENA upload tool from metadata templates</description>
    <requirements>
        <container type="docker">neoformit/ena-upload:v1.0</container>
    </requirements>
    <entry_points>
        <entry_point name="ENA upload table builder" requires_domain="True">
            <port>5173</port>
        </entry_point>
    </entry_points>
    <command detect_errors="exit_code"><![CDATA[

## When these files are created, the app will automatically terminate:
#set temp_output_study = "/app/study_table.tsv"
#set temp_output_experiment = "/app/experiment_table.tsv"
#set temp_output_run = "/app/run_table.tsv"
#set temp_output_sample = "/app/sample_table.tsv"

#if $input_tsv.select_input_tsvs:
    #if $input_tsv.input_study_table:
        ENA_INPUT_STUDY='$input_tsv.input_study_table'
    #end if
    #if $input_tsv.input_experiment_table:
        ENA_INPUT_EXPERIMENT='$input_tsv.input_experiment_table'
    #end if
    #if $input_tsv.input_run_table:
        ENA_INPUT_RUN='$input_tsv.input_run_table'
    #end if
    #if $input_tsv.input_sample_table:
        ENA_INPUT_SAMPLE='$input_tsv.input_sample_table'
    #end if
#end if

ENA_OUTPUT_STUDY='$temp_output_study'
ENA_OUTPUT_EXPERIMENT='$temp_output_experiment'
ENA_OUTPUT_RUN='$temp_output_run'
ENA_OUTPUT_SAMPLE='$temp_output_sample'
/app/run.sh

&& cp $temp_output_study      '${output_study_table}'
&& cp $temp_output_experiment '${output_experiment_table}'
&& cp $temp_output_run        '${output_run_table}'
&& cp $temp_output_sample     '${output_sample_table}'

    ]]></command>
    <inputs>
        <conditional name="input_tsv">
        <param name="select_input_tsvs" type="boolean" checked="false" label="Edit existing tables" help="If you have partially-filled tables that you would like to complete, you can pass them to the app. You will need to know which metadata template your tables have been built against, and select it when the tool launches. It is HIGHLY recommended that these files come from a previous run of this tool, but any table will work if the schema is correct. You do not have to pass all four table if you don't have data for all of them." />
            <when value="true">
                <param name="input_study_table" type="data" format="tabular" label="Study table" optional="true" />
                <param name="input_experiment_table" type="data" format="tabular" label="Experiment table" optional="true" />
                <param name="input_run_table" type="data" format="tabular" label="Run table" optional="true" />
                <param name="input_sample_table" type="data" format="tabular" label="Sample table" optional="true" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_study_table" label="Study table" format="tabular" />
        <data name="output_experiment_table" label="Experiment table" format="tabular" />
        <data name="output_run_table" label="Run table" format="tabular" />
        <data name="output_sample_table" label="Sample table" format="tabular" />
    </outputs>
    <help>
<![CDATA[

.. class:: infomark

**What it does**

*This interactive tool has been designed to allow user to efficiently produce the metadata tables you need to support a submission to ENA*

**Requirement**

- Submission to ENA requires an existing account at EBI/ENA and have saved those account details into your Galaxy User Preferences. Help on this process is here `ENA account registration <https://ena-docs.readthedocs.io/en/latest/submit/general-guide/registration.html>`_ and `Galaxy User Preference <https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html>`_.

**Tool usage**

- It allows users to create and edit the Study, Samples, Experiments and Run metadata table. The metadata tables will be exported to the Galaxy history.

- After use of this tool, submission to ENA is best handled inside Galaxy through the ENA Upload tool `Github repository <https://github.com/usegalaxy-eu/ena-upload-cli>`_.

- This tool provides for New Submission or Edit/Updating existing submission

1) New Submission - blank templates can be found `here <https://github.com/ELIXIR-Belgium/ENA-metadata-templates/tree/main/templates>`_.

2) The detail of each templates can found found `here <https://www.ebi.ac.uk/ena/browser/checklists>`_.

**Notes:**

Edit/Updating - pick single or multiple files from current History. These files are HIGHLY recommended to have been generated from a previous session of New Submission. However the tool will accept template files you have prepared elsewhere

]]>
    </help>
</tool>