comparison ena_upload.xml @ 2:9e2df763086c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"

1:57251c760cab

<tool id="ena_upload" name="ENA Upload tool" version="0.3.1" profile="20.01" license="MIT">
    <macros>
        <token name="@VERSION@">0.2.7</token>
        <import>samples_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
        <requirement type="package" version="1.2.0">xlrd</requirement>

    ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
    ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
    ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
    ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
#end if


#if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
    webin_id=`grep 'username' $credentials`;
    if [ "\$webin_id" = "" ]; then
      ## No credentials in user defined preferences    

            </output>
            <output name="samples_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="18"/>
                    <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tcollection_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tsubmission_date"/>
                </assert_contents>
            </output>
            <output name="runs_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>

            </output>
            <output name="samples_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="8"/>
                        <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tsubmission_date"/>
                </assert_contents>
            </output>
            <output name="runs_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>

    </tests>
    <help><![CDATA[
        This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
        The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
        It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing
        For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1U4VdcczsIecIXxseV8svE1zO_CBUadog/view?usp=sharing 
    ]]></help>
    <citations>
    </citations>
</tool>

2:9e2df763086c

<tool id="ena_upload" name="ENA Upload tool" version="0.3.2" profile="20.01" license="MIT">
    <macros>
        <token name="@VERSION@">0.3.1</token>
        <import>samples_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
        <requirement type="package" version="1.2.0">xlrd</requirement>

    ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path &&
    ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path &&
    ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path &&
    ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path &&
#end if

#if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
    webin_id=`grep 'username' $credentials`;
    if [ "\$webin_id" = "" ]; then
      ## No credentials in user defined preferences    

            </output>
            <output name="samples_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="18"/>
                    <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date"/>
                </assert_contents>
            </output>
            <output name="runs_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="8"/>
                    <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
                    <has_line_matching expression="r_(.*)_026\tadd\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/>
                </assert_contents>
            </output>
        </test>
        <!--Test excel input of VIRAL samples with extended columns-->
        <test>
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />
                    <param name="dry_run" value="true" />
                </section>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="excel_tables"/>
                    <param name="viral_submission" value="True"/>
                    <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
                    <conditional name="run_input_format_conditional">
                        <param name="run_input_format" value="multiple_selection_list"/>
                        <param name="data" value="sample.fq"/>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <output name="experiments_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="17"/>
                    <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\tsubmission_date" />
                    <has_line_matching expression="e_(.*)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/>
                </assert_contents>
            </output>
            <output name="studies_table_out">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_n_columns n="8"/>
                    <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/>
                    <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/>
                </assert_contents>
            </output>
            <output name="samples_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="42"/>
                    <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date\tgeographic_location_latitude\tgeographic_location_longitude\tsample_capture_status\thost_disease_outcome\thost_age\tvirus_identifier\treceipt_date\tdefinition_for_seropositive_sample\tserotype\thost_habitat\tisolation_source_host_associated\thost_behaviour\tisolation_source_non_host_associated\tsubject_exposure\tsubject_exposure_duration\ttype_exposure\tpersonal_protective_equipment\thospitalisation\tillness_duration\tillness_symptoms\tsample_storage_conditions\tstrain\thost_description\tgravidity"/>
                </assert_contents>
            </output>
            <output name="runs_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>

            </output>
            <output name="samples_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_n_columns n="8"/>
                        <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/>
                </assert_contents>
            </output>
            <output name="runs_table_out">
                <assert_contents>
                    <has_n_lines n="5"/>

    </tests>
    <help><![CDATA[
        This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
        The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
        It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing
        For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing
    ]]></help>
    <citations>
    </citations>
</tool>