comparison samples_macros.xml @ 2:2f7a70c0d3ab draft default tip

Uploaded

1:9681a9180730

        </conditional>
    </xml>
    <xml name="table_inputs_macro">
        <conditional name="input_format_conditional">
            <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
                <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option>
                <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
                <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
            </param>
            <when value="excel_tables">
                <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
                <expand macro="checklist_input_macro"/>
                <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" />
                <expand macro="run_inputs_macro" />
            </when>
            <when value="user_generated_tables">
                <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
                <expand macro="checklist_input_macro"/>

        <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
        <repeat name="rep_sample" title="Samples associated with this study" min="1" >
            <param name="sample_title" type="text" label="Sample title"/>
            <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
            <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
            <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
            <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
                <param name="experiment_title" type="text" label="Specify an experiment title" />
                <param name="experiment_design" type="text" label="Describe the experiment design" />
                <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
                    <options from_data_table="library_strategy">

2:2f7a70c0d3ab

        </conditional>
    </xml>
    <xml name="table_inputs_macro">
        <conditional name="input_format_conditional">
            <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
                <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option>
                <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
                <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
            </param>
            <when value="excel_tables">
                <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
                <expand macro="checklist_input_macro"/>
                <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" />
                <expand macro="run_inputs_macro" />
            </when>
            <when value="user_generated_tables">
                <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
                <expand macro="checklist_input_macro"/>

        <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
        <repeat name="rep_sample" title="Samples associated with this study" min="1" >
            <param name="sample_title" type="text" label="Sample title"/>
            <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
            <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
            <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
            <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
                <param name="experiment_title" type="text" label="Specify an experiment title" />
                <param name="experiment_design" type="text" label="Describe the experiment design" />
                <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
                    <options from_data_table="library_strategy">