comparison samples_macros.xml @ 4:26ccb678abc8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"

3:59bb6d34fca6

            <param name="run_input_format" type="select" label="Select runs input format">
                <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
                <option value="paired_list" selected="False">Input from a paired collection</option>
            </param>
            <when value="multiple_selection_list">
                <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
            </when>
            <when value="paired_list">
                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" />
            </when>
        </conditional>
    </xml>
    <xml name="table_inputs_macro">
        <conditional name="input_format_conditional">

                <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
                <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
                <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
            </when>
            <when value="build_tables">
                <conditional name="conditional_viral_metadata">
                    <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
                    <when value="true">
                        <expand macro="viral_samples" />
                    </when>

                        <options from_data_table="instrument_model">
                            <column name="value" index="0"/>
                        </options>
                    </param>
                    <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
                        <param name="run_base_name" type="text" optional="False" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
                        <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                    </repeat>
                </repeat>
            </repeat>
        </repeat>
    </xml>

                    <options from_data_table="instrument_model">
                        <column name="value" index="0"/>
                    </options>
                </param>
                <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
                    <param name="run_base_name" type="text" optional="False" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
                    <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                </repeat>
            </repeat>
        </repeat>
    </repeat>
    </xml>

4:26ccb678abc8

            <param name="run_input_format" type="select" label="Select runs input format">
                <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
                <option value="paired_list" selected="False">Input from a paired collection</option>
            </param>
            <when value="multiple_selection_list">
                <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
                <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
            </when>
            <when value="paired_list">
                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" />
            </when>
        </conditional>
    </xml>
    <xml name="table_inputs_macro">
        <conditional name="input_format_conditional">

                <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
                <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
                <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
            </when>
            <when value="build_tables">
                <param name="add_extension" type="boolean" checked="false" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
                <conditional name="conditional_viral_metadata">
                    <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
                    <when value="true">
                        <expand macro="viral_samples" />
                    </when>

                        <options from_data_table="instrument_model">
                            <column name="value" index="0"/>
                        </options>
                    </param>
                    <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
                        <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
                        <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                    </repeat>
                </repeat>
            </repeat>
        </repeat>
    </xml>

                    <options from_data_table="instrument_model">
                        <column name="value" index="0"/>
                    </options>
                </param>
                <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
                    <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
                    <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                </repeat>
            </repeat>
        </repeat>
    </repeat>
    </xml>