comparison ena_upload.xml @ 4:26ccb678abc8 draft

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

3:59bb6d34fca6

<tool id="ena_upload" name="ENA Upload tool" version="0.3.3" 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>

#if $action_options.input_format_conditional.input_format == "excel_tables":
    python '$__tool_directory__/process_xlsx.py'
    #if $action_options.input_format_conditional.viral_submission == "true":
        --vir 
    #end if
    --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
#end if

#if $action_options.input_format_conditional.input_format != "user_generated_tables":
    cp $studies_table_path $studies_table_out &&

      #for $sample in $study.rep_sample:
        #for $experiment in $sample.rep_experiment:
          #for $run in $experiment.rep_runs:
            #for $file in $run.upload_files:
                #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
                ln -s '$file' $safename_reads_file &&
                $files_to_upload.append(str($safename_reads_file))
            #end for
          #end for
        #end for
      #end for
    #end for
#else:
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
        #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
            #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.gz'
            #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq.bz2'
            #else:
                #set $safename_fwd_reads_file = $safename_reads_file + '_1.fastq'
            #end if
            #if $pair.reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
                #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.gz'
            #elif $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq.bz2'
            #else:
                #set $safename_rev_reads_file = $safename_reads_file + '_2.fastq'
            #end if

            ln -s '$pair.forward' $safename_fwd_reads_file &&
            $files_to_upload.append(str($safename_fwd_reads_file))
            ln -s '$pair.reverse' $safename_rev_reads_file &&
            $files_to_upload.append(str($safename_rev_reads_file))
        #end for
    #end if
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
        #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
            ln -s '$file' $safename_reads_file &&
            $files_to_upload.append(str($safename_reads_file))
        #end for
    #end if
#end if


#if $action_options.test_submit_parameters.dry_run == "false":
ena-upload-cli
    --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
    --action '$action_options.action'
    --center '$action_options.center'
    --secret \${credentials_path}
    --data
    #for $dataset in $files_to_upload:
        '$dataset'
    #end for
--experiment '$experiments_table_path'
--study '$studies_table_path'
--run '$runs_table_path'
--sample '$samples_table_path'
#if $action_options.input_format_conditional.input_format == "user_generated_tables":
    #if "$action_options.input_format_conditional.viral_submission" == "true":
        --vir
    #end if
#else:
    #if $action_options.input_format_conditional.input_format == "build_tables":
        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
          --vir
        #end if
    #else:
        #if $action_options.input_format_conditional.viral_submission == "true":
          --vir
        #end if
    #end if
#end if

#if $action_options.test_submit_parameters.submit_dev == "true":
    -d
#end if
    >> '$output';
    echo -e 'center_name\t$action_options.center' >> '$output';
    echo -e 'action_option\t$action_options.action' >> '$output';
    #if $action_options.input_format_conditional.input_format != "user_generated_tables":
        cp $studies_table_path_updated $studies_table_out 2>/dev/null;
        cp $samples_table_path_updated $samples_table_out 2>/dev/null;

                <param name="test_submit" type="hidden" value="False" />
                <expand macro="table_inputs_macro" />
            </when>
            <when value="modify">
                <expand macro="test_submit_section"/>    
                <expand macro="table_inputs_macro" />
            </when>
        </conditional>
    </inputs>
    <outputs>

        <data name="runs_table_out" format="tabular" label="Runs table">
            <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
        </data>
    </outputs>
    <tests>
        <!--Test excel input of VIRAL samples -->
        <test>
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />

                <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.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>

            <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="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" />

                <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>

            <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"/>
                    <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 NON-VIRAL samples-->
        <test>
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />

                <conditional name="input_format_conditional">
                    <param name="input_format" value="excel_tables"/>
                    <param name="viral_submission" value="False"/>
                    <param name="xlsx_file" value="metadata_test_nonviral.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>

            <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 failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
        <test expect_failure="true">
            <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="false" />
                </section>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="excel_tables"/>
                    <param name="viral_submission" value="False"/>
                    <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
                    <conditional name="run_input_format_conditional">
                        <param name="run_input_format" value="paired_list"/>

                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
            </assert_command>
        </test>
        <!--Test build tables from user input fields NON-VIRAL samples-->
        <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="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="False"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>
                            <param name="study_abstract" value="Test study abstract"/>

                    <has_n_columns n="8"/>
                    <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
                </assert_contents>
            </output>
        </test>
        <!--Test RUN failing build tables from user input fields NON-VIRAL samples-->
        <test expect_failure="true">
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="true" />
                    <param name="dry_run" value="false" />
                </section>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="false"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>
                            <param name="study_abstract" value="Test study abstract"/>

            <param name="center" value="Some research center"/>
            <assert_stdout>
                <has_text_matching expression="No ENA credentials defined"/>
            </assert_stdout>
        </test>
        <!--Test with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples-->
        <test expect_failure="true">
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="true" />
                    <param name="dry_run" value="false" />
                </section>
                <param name="test_submit" value="True"/>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="false"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>

                                    <param name="library_construction_protocol" value="Test library construction"/>
                                    <param name="platform" value="ILLUMINA"/>
                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                    <repeat name="rep_runs">
                                        <param name="run_base_name" value="run_from_hospital_X"/>
                                        <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
                                    </repeat>
                                </repeat>
                            </repeat>
                        </repeat>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <assert_command>
                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
            </assert_command>
            <assert_stderr>
                <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
            </assert_stderr>
        </test>
        <!--test viral submission - User input metadata-->
        <test expect_failure="true">
            <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="false" />
                </section>
                <param name="test_submit" value="True"/>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="True"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>

                                    <param name="library_construction_protocol" value="Test library construction"/>
                                    <param name="platform" value="ILLUMINA"/>
                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                    <repeat name="rep_runs">
                                        <param name="run_base_name" value="run_from_hospital_X"/>
                                        <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
                                    </repeat>
                                </repeat>
                            </repeat>
                        </repeat>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <assert_command>
                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data '1.fastqsanger.gz' 'sample.fq'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
                <has_text_matching expression="--vir"/>
            </assert_command>
            <assert_stderr>
                <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
            </assert_stderr>
        </test>

4:26ccb678abc8

<tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">
    <macros>
        <token name="@VERSION@">0.4.1</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>

#if $action_options.input_format_conditional.input_format == "excel_tables":
    python '$__tool_directory__/process_xlsx.py'
    #if $action_options.input_format_conditional.viral_submission == "true":
        --vir 
    #end if
    #if $action_options.test_submit_parameters.submit_dev == "true":
        --dev
    #end if
    --action '$action_options.action' --form '$action_options.input_format_conditional.xlsx_file' --out_dir ./submission_files --verbose > '$output';
#end if

#if $action_options.input_format_conditional.input_format != "user_generated_tables":
    cp $studies_table_path $studies_table_out &&

      #for $sample in $study.rep_sample:
        #for $experiment in $sample.rep_experiment:
          #for $run in $experiment.rep_runs:
            #for $file in $run.upload_files:
                #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
                #if $action_options.input_format_conditional.add_extension == "true":
                    #set $extension = '.fastq'
                #else
                    #set $extension = ''
                #end if
                #if $file.is_of_type('fastq', 'fastqsanger'):
                    ## compression output is defined as safename_reads_file so no need to symlink
                    #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
                    gzip -c '$file' > $safename_reads_file &&
                #else:
                    #if $action_options.input_format_conditional.add_extension == "true":
                        #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                            #set $compression = '.gz' 
                        #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                            #set $compression = '.bz2' 
                        #end if
                        #set $safename_reads_file = $safename_reads_file + $extension + $compression 
                    #end if
                    ln -s '$file' $safename_reads_file &&
                #end if
                $files_to_upload.append(str($safename_reads_file))
            #end for
          #end for
        #end for
      #end for
    #end for
#else:
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list':
        #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name)
            ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions
            #if $pair.forward.is_of_type('fastq', 'fastqsanger'):
                ## compress the file, no need to create the link then
                ## always add the compression suffix (.gz)
                #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz'
                gzip -c '$file' > $safename_fwd_reads_file &&
            #else
                #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                    #set $compression = '.gz'
                #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                    #set $compression = '.bz2'
                #end if
                #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression
                ln -s '$pair.forward' $safename_fwd_reads_file &&
            #end if

            #if $pair.reverse.is_of_type('fastq', 'fastqsanger'):
                ## compress the file, no need to create the link then
                #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz'
                gzip -c '$file' > $safename_rev_reads_file &&
            #else
                #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                    #set $compression = '.bz2'
                #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'):
                    #set $compression = '.gz'
                #end if
                #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression
                ln -s '$pair.reverse' $safename_rev_reads_file &&
            #end if
            $files_to_upload.append(str($safename_fwd_reads_file))
            $files_to_upload.append(str($safename_rev_reads_file))
        #end for
    #end if
    #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list':
        #for $file in $action_options.input_format_conditional.run_input_format_conditional.data:
            #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
            #if $file.is_of_type('fastq', 'fastqsanger'):
                ## always compress add the gz extension
                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
                    #set $safename_reads_file = $safename_reads_file + 'fastq.gz'
                #else
                    #set $safename_reads_file = $safename_reads_file + '.gz'
                #end if   
                gzip -c '$file' > $safename_reads_file &&
            #else
                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
                    #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                        #set $extension = 'fastq.gz'
                    #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
                        #set $extension = 'fastq.bz2'
                    #end if
                    #set $safename_reads_file = $safename_reads_file + $extension
                #end if
                ln -s '$file' $safename_reads_file &&
            #end if      
            $files_to_upload.append(str($safename_reads_file))
        #end for
    #end if
#end if


#if $action_options.test_submit_parameters.dry_run == "false":
#if $action_options.action == "add":
ena-upload-cli
    --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
    --action '$action_options.action'
    --center '$action_options.center'
    --secret \${credentials_path}
    --data
    #for $dataset in $files_to_upload:
        '$dataset'
    #end for
--action add
--experiment '$experiments_table_path'
--study '$studies_table_path'
--run '$runs_table_path'
--sample '$samples_table_path'
#if $action_options.input_format_conditional.input_format == "user_generated_tables":
    #if "$action_options.input_format_conditional.viral_submission" == "true":
        --checklist ERC000033
    #end if
#else:
    #if $action_options.input_format_conditional.input_format == "build_tables":
        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
          --checklist ERC000033
        #end if
    #else:
        #if $action_options.input_format_conditional.viral_submission == "true":
          --checklist ERC000033
        #end if
    #end if
#end if

#if $action_options.test_submit_parameters.submit_dev == "true":
    -d
#end if
    >> '$output';
#end if

#if $action_options.action == "modify":
    ena-upload-cli
    --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
    --action '$action_options.action'
    --center '$action_options.center'
    --secret \${credentials_path}
    --data
    #for $dataset in $files_to_upload:
        '$dataset'
    #end for
--action 'modify'
--experiment '$experiments_table_path'
--study '$studies_table_path'
--run '$runs_table_path'
--sample '$samples_table_path'
#if $action_options.input_format_conditional.input_format == "user_generated_tables":
    #if "$action_options.input_format_conditional.viral_submission" == "true":
        --checklist ERC000033
    #end if
#else:
    #if $action_options.input_format_conditional.input_format == "build_tables":
        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
          --checklist ERC000033
        #end if
    #else:
        #if $action_options.input_format_conditional.viral_submission == "true":
          --checklist ERC000033
        #end if
    #end if
#end if
    >> '$output';
#end if
    echo -e 'center_name\t$action_options.center' >> '$output';
    echo -e 'action_option\t$action_options.action' >> '$output';
    #if $action_options.input_format_conditional.input_format != "user_generated_tables":
        cp $studies_table_path_updated $studies_table_out 2>/dev/null;
        cp $samples_table_path_updated $samples_table_out 2>/dev/null;

                <param name="test_submit" type="hidden" value="False" />
                <expand macro="table_inputs_macro" />
            </when>
            <when value="modify">
                <expand macro="test_submit_section"/>    
                <param name="test_submit" type="hidden" value="False" />
                <expand macro="table_inputs_macro" />
            </when>
        </conditional>
    </inputs>
    <outputs>

        <data name="runs_table_out" format="tabular" label="Runs table">
            <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter>
        </data>
    </outputs>
    <tests>
        <!--Test 1:  excel input of VIRAL samples -->
        <test>
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />

                <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.xlsx"/>
                    <conditional name="run_input_format_conditional">
                        <param name="add_extension" value="true"/>
                        <param name="run_input_format" value="multiple_selection_list"/>
                        <param name="data" value="sample.fq"/>
                    </conditional>
                </conditional>
            </conditional>

            <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\tmodify\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\tmodify\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="18"/>
                </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\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 2: 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" />

                <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="add_extension" value="true"/>
                        <param name="run_input_format" value="multiple_selection_list"/>
                        <param name="data" value="sample.fq"/>
                    </conditional>
                </conditional>
            </conditional>

            <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\tmodify\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\tmodify\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"/>
                </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\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 3: excel input of NON-VIRAL samples-->
        <test>
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />

                <conditional name="input_format_conditional">
                    <param name="input_format" value="excel_tables"/>
                    <param name="viral_submission" value="False"/>
                    <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
                    <conditional name="run_input_format_conditional">
                        <param name="add_extension" value="true"/>
                        <param name="run_input_format" value="multiple_selection_list"/>
                        <param name="data" value="sample.fq"/>
                    </conditional>
                </conditional>
            </conditional>

            <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\tmodify\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\t\tsubmission_date_ENA"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
        <test expect_failure="true">
            <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="false" />
                </section>
                <conditional name="input_format_conditional">
                    <param name="add_extension" value="true"/>
                    <param name="input_format" value="excel_tables"/>
                    <param name="viral_submission" value="False"/>
                    <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
                    <conditional name="run_input_format_conditional">
                        <param name="run_input_format" value="paired_list"/>

                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
            </assert_command>
        </test>
        <!--Test 5: build tables from user input fields NON-VIRAL samples-->
        <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="build_tables"/>
                    <param name="add_extension" value="true"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="False"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>
                            <param name="study_abstract" value="Test study abstract"/>

                    <has_n_columns n="8"/>
                    <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples-->
        <test expect_failure="true">
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="true" />
                    <param name="dry_run" value="false" />
                </section>
                <conditional name="input_format_conditional">
                    <param name="input_format" value="build_tables"/>
                    <param name="add_extension" value="true"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="false"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>
                            <param name="study_abstract" value="Test study abstract"/>

            <param name="center" value="Some research center"/>
            <assert_stdout>
                <has_text_matching expression="No ENA credentials defined"/>
            </assert_stdout>
        </test>
        <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
            also tests compression of uncompressed inputs and adding the .gz suffix -->
        <test expect_failure="true">
            <conditional name="action_options">
                <param name="action" value="add"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="true" />
                    <param name="dry_run" value="false" />
                </section>
                <param name="test_submit" value="True"/>
                <conditional name="input_format_conditional">
                    <param name="add_extension" value="true"/>
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="false"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>

                                    <param name="library_construction_protocol" value="Test library construction"/>
                                    <param name="platform" value="ILLUMINA"/>
                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                    <repeat name="rep_runs">
                                        <param name="run_base_name" value="run_from_hospital_X"/>
                                        <param name="upload_files" value="sample.fq,sample.fq" ftype="fastqsanger"/>
                                    </repeat>
                                </repeat>
                            </repeat>
                        </repeat>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <assert_command>
                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data 'sample.fq.fastq.gz' 'sample.fq.fastq.gz'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
                <not_has_text text="modify" />
            </assert_command>
            <assert_stderr>
                <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
            </assert_stderr>
        </test>
        <!--Test 8: viral submission - User input metadata - Add extension = False-->
        <test expect_failure="true">
            <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="false" />
                </section>
                <param name="test_submit" value="True"/>
                <conditional name="input_format_conditional">
                    <param name="add_extension" value="False"/>
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="true"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>
                            <param name="study_abstract" value="Test study abstract"/>
                            <param name="study_type" value="Epigenetics"/>
                            <param name="study_pubmed_id" value="Test study pubmedID"/>
                            <repeat name="rep_sample">
                                <param name="sample_title" value="Test Sample title"/>
                                <param name="sample_description" value="Test Sample description"/>
                                <param name="scientific_name" value="Test Sample scientific name"/>
                                <param name="tax_id" value="Test Sample tax_id"/>
                                <param name="collection_date" value="2020"/>
                                <param name="geo_location_country" value="Belgium"/>
                                <param name="host_common_name" value="Human"/>
                                <param name="host_subject_id" value="Patient_001"/>
                                <param name="host_health_state" value="healthy"/>
                                <param name="host_sex" value="female"/>
                                <param name="host_scientific_name" value="homo sapiens"/>
                                <param name="collector_name" value="John The Collector"/>
                                <param name="collecting_institution" value="Hospital 01"/>
                                <param name="isolate" value="sample_001"/>
                                <repeat name="rep_experiment">
                                    <param name="experiment_title" value="Test experiment title"/>
                                    <param name="experiment_design" value="Test experiment design description"/>
                                    <param name="library_strategy" value="CTS"/>
                                    <param name="library_source" value="GENOMIC"/>
                                    <param name="library_selection" value="PCR"/>
                                    <param name="library_layout" value="SINGLE"/>
                                    <param name="insert_size" value="150"/>
                                    <param name="library_construction_protocol" value="Test library construction"/>
                                    <param name="platform" value="ILLUMINA"/>
                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                    <repeat name="rep_runs">
                                        <param name="run_base_name" value="run_from_hospital_X"/>
                                        <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
                                    </repeat>
                                </repeat>
                            </repeat>
                        </repeat>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <assert_command>
                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
                <has_text_matching expression="--checklist ERC000033"/>
            </assert_command>
            <assert_stderr>
                <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
            </assert_stderr>
        </test>
        <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
        <test expect_failure="true">
            <conditional name="action_options">
                <param name="action" value="modify"/>
                <section name="test_submit_parameters">
                    <param name="submit_dev" value="false" />
                    <param name="dry_run" value="false" />
                </section>
                <param name="test_submit" value="True"/>
                <conditional name="input_format_conditional">
                    <param name="add_extension" value="False"/>
                    <param name="input_format" value="build_tables"/>
                    <conditional name="conditional_viral_metadata">
                        <param name="viral_sample" value="True"/>
                        <repeat name="rep_study">
                            <param name="study_title" value="Test study title"/>

                                    <param name="library_construction_protocol" value="Test library construction"/>
                                    <param name="platform" value="ILLUMINA"/>
                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                    <repeat name="rep_runs">
                                        <param name="run_base_name" value="run_from_hospital_X"/>
                                        <param name="upload_files" value="sample.fq" ftype="fastqsanger"/>
                                    </repeat>
                                </repeat>
                            </repeat>
                        </repeat>
                    </conditional>
                </conditional>
            </conditional>
            <param name="center" value="Some research center"/>
            <assert_command>
                <has_text_matching expression="ena-upload-cli"/>
                <has_text_matching expression="--data 'sample.fq.gz'"/>
                <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
                <has_text_matching expression="--checklist ERC000033"/>
                <not_has_text text="add" />
            </assert_command>
            <assert_stderr>
                <has_text_matching expression="Oops, the file test_fake_path does not exist"/>
            </assert_stderr>
        </test>