Mercurial > repos > iuc > ena_upload
diff ena_upload.xml @ 7:6f6537780379 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
| author | iuc |
|---|---|
| date | Thu, 24 Feb 2022 18:20:40 +0000 |
| parents | 4aab5ae907b6 |
| children | d147d6455873 |
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--- a/ena_upload.xml Mon Nov 15 11:47:13 2021 +0000 +++ b/ena_upload.xml Thu Feb 24 18:20:40 2022 +0000 @@ -1,11 +1,10 @@ <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT"> <macros> - <token name="@VERSION@">0.4.3</token> + <token name="@VERSION@">0.5.3</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> </requirements> <stdio> <regex match="Oops" source="stderr" level="fatal"/> @@ -27,30 +26,27 @@ #if $action_options.input_format_conditional.input_format == "build_tables": python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; #end if + +credentials_path='test_fake_path'; +echo "username: test_user" > \$credentials_path; +echo "password: test_password" >> \$credentials_path; -#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": +#if $action_options.input_format_conditional.input_format == "build_tables": cp $studies_table_path $studies_table_out && cp $samples_table_path $samples_table_out && cp $experiments_table_path $experiments_table_out && cp $runs_table_path $runs_table_out && -#else: +#end if +#if $action_options.input_format_conditional.input_format == "user_generated_tables": ln -s '$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 $action_options.input_format_conditional.input_format == "excel_tables": + ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx && +#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 @@ -73,9 +69,6 @@ fi; #end if -#if $action_options.test_submit == "True": - credentials_path='test_fake_path'; -#end if ## create the list of files to upload and make the symlinks #import re @@ -156,7 +149,7 @@ #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' + #set $safename_reads_file = $safename_reads_file + '.fastq.gz' #else #set $safename_reads_file = $safename_reads_file + '.gz' #end if @@ -164,9 +157,9 @@ #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' + #set $extension = '.fastq.gz' #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): - #set $extension = 'fastq.bz2' + #set $extension = '.fastq.bz2' #end if #set $safename_reads_file = $safename_reads_file + $extension #end if @@ -177,8 +170,6 @@ #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' @@ -189,24 +180,27 @@ #for $dataset in $files_to_upload: '$dataset' #end for +#if $action_options.test_submit_parameters.dry_run == "true": + --draft +#end if +#if $action_options.input_format_conditional.input_format != "excel_tables": + --experiment '$experiments_table_path' + --study '$studies_table_path' + --run '$runs_table_path' + --sample '$samples_table_path' +#else + --xlsx ./xlsx_input.xlsx +#end if --action add ---experiment '$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 + --checklist $action_options.input_format_conditional.checklist_id #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 + --checklist $action_options.input_format_conditional.checklist_id #end if #end if @@ -216,6 +210,8 @@ >> '$output'; #end if + + #if $action_options.action == "modify": ena-upload-cli --tool 'ena-upload-cli v@VERSION@ @ Galaxy' @@ -226,40 +222,54 @@ #for $dataset in $files_to_upload: '$dataset' #end for +#if $action_options.test_submit_parameters.dry_run == "true": + --draft +#end if +#if $action_options.input_format_conditional.input_format != "excel_tables": + --experiment '$experiments_table_path' + --study '$studies_table_path' + --run '$runs_table_path' + --sample '$samples_table_path' +#else + --xlsx ./xlsx_input.xlsx + --auto_action +#end if --action 'modify' ---experiment '$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 + --checklist $action_options.input_format_conditional.checklist_id #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 + --checklist $action_options.input_format_conditional.checklist_id #end if #end if >> '$output'; #end if + +#if $action_options.test_submit_parameters.dry_run == "false": echo -e 'center_name\t$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; - cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; - cp $runs_table_path_updated $runs_table_out 2>/dev/null; - #end if -#else: - exit 0; +#end if + +## copy updated files +#if $action_options.input_format_conditional.input_format == "excel_tables": + ## for the excel input case, copy the upload-cli generated tables to the output files + ## this applies for both draft and real submissions + cp './ENA_template_experiment_updated.tsv' $experiments_table_out; + cp './ENA_template_sample_updated.tsv' $samples_table_out; + cp './ENA_template_study_updated.tsv' $studies_table_out; + cp './ENA_template_run_updated.tsv' $runs_table_out; +#else + cp $studies_table_path_updated $studies_table_out 2>/dev/null; + cp $samples_table_path_updated $samples_table_out 2>/dev/null; + cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; + cp $runs_table_path_updated $runs_table_out 2>/dev/null; #end if +python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output; ]]></command> <configfiles> <configfile name="credentials"><![CDATA[ @@ -341,7 +351,7 @@ </data> </outputs> <tests> - <!--Test 1: excel input of VIRAL samples --> + <!--Test 1: excel input of VIRAL samples --> <test> <conditional name="action_options"> <param name="action" value="add"/> @@ -351,12 +361,12 @@ </section> <conditional name="input_format_conditional"> <param name="input_format" value="excel_tables"/> - <param name="viral_submission" value="True"/> + <param name="checklist_id" value="ERC000033"/> <param name="xlsx_file" value="metadata_test_viral.xlsx"/> <conditional name="run_input_format_conditional"> - <param name="add_extension" value="true"/> + <param name="add_extension" value="false"/> <param name="run_input_format" value="multiple_selection_list"/> - <param name="data" value="sample.fq"/> + <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> </conditional> </conditional> </conditional> @@ -365,16 +375,15 @@ <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_(.*)"/> + <has_line_matching expression="alias\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\taccession\tsubmission_date\tstatus"/> + <has_line_matching expression="e_(.*)_026\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(.*)"/> + <has_n_columns n="7"/> + <has_line_matching expression="SARS-CoV-2_genomes_01\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"> @@ -387,8 +396,8 @@ <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"/> + <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> + <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> </assert_contents> </output> </test> @@ -402,12 +411,12 @@ </section> <conditional name="input_format_conditional"> <param name="input_format" value="excel_tables"/> - <param name="viral_submission" value="True"/> + <param name="checklist_id" value="ERC000033"/> <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="add_extension" value="false"/> <param name="run_input_format" value="multiple_selection_list"/> - <param name="data" value="sample.fq"/> + <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> </conditional> </conditional> </conditional> @@ -416,30 +425,39 @@ <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_(.*)"/> + <has_line_matching expression="alias\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\taccession\tsubmission_date\tstatus"/> + <has_line_matching expression="e_(.*)_026\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(.*)"/> + <has_n_columns n="7"/> + <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> + <has_line_matching expression="SARS-CoV-2_genomes_01\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_n_columns n="43"/> </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"/> + <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> + <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> + </assert_contents> + </output> + <output name="output"> + <assert_contents> + <has_line_matching expression="YAML -------------"/> + <has_line_matching expression="ENA_experiment:"/> + <has_line_matching expression="ENA_sample:"/> + <has_line_matching expression="ENA_study:"/> + <has_line_matching expression="ENA_run:"/> </assert_contents> </output> </test> @@ -453,43 +471,43 @@ </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"/> + <param name="checklist_id" value="ERC000011"/> + <param name="xlsx_file" value="metadata_test_nonviral_1_run.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"/> + <param name="data" value="sample_no_extension"/> </conditional> </conditional> </conditional> <param name="center" value="Some research center"/> <output name="experiments_table_out"> <assert_contents> - <has_n_lines n="5"/> + <has_n_lines n="2"/> <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="alias\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\taccession\tsubmission_date\tstatus"/> </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_n_columns n="7"/> + <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> </assert_contents> </output> <output name="samples_table_out"> <assert_contents> - <has_n_lines n="5"/> + <has_n_lines n="2"/> <has_n_columns n="8"/> - <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/> + <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/> </assert_contents> </output> <output name="runs_table_out"> <assert_contents> - <has_n_lines n="5"/> + <has_n_lines n="2"/> <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"/> + <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> + <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/> </assert_contents> </output> </test> @@ -504,7 +522,7 @@ <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="checklist_id" value="ERC000011"/> <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> <conditional name="run_input_format_conditional"> <param name="run_input_format" value="paired_list"/> @@ -538,7 +556,7 @@ </section> <conditional name="input_format_conditional"> <param name="input_format" value="build_tables"/> - <param name="add_extension" value="true"/> + <param name="add_extension" value="false"/> <conditional name="conditional_viral_metadata"> <param name="viral_sample" value="False"/> <repeat name="rep_study"> @@ -550,7 +568,7 @@ <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="tax_id" value="2697049"/> <repeat name="rep_experiment"> <param name="experiment_title" value="Test experiment title"/> <param name="experiment_design" value="Test experiment design description"/> @@ -563,7 +581,7 @@ <param name="platform" value="ILLUMINA"/> <param name="instrument_model" value="Illumina HiSeq 4000"/> <repeat name="rep_runs"> - <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/> + <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger.gz"/> </repeat> </repeat> </repeat> @@ -621,7 +639,7 @@ <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="tax_id" value="2697049"/> <repeat name="rep_experiment"> <param name="experiment_title" value="Test experiment title"/> <param name="experiment_design" value="Test experiment design description"/> @@ -649,16 +667,16 @@ </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"> + <test expect_failure="false"> <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" /> + <param name="dry_run" value="true" /> </section> <param name="test_submit" value="True"/> <conditional name="input_format_conditional"> - <param name="add_extension" value="true"/> + <param name="add_extension" value="false"/> <param name="input_format" value="build_tables"/> <conditional name="conditional_viral_metadata"> <param name="viral_sample" value="false"/> @@ -671,7 +689,7 @@ <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="tax_id" value="2697049"/> <repeat name="rep_experiment"> <param name="experiment_title" value="Test experiment title"/> <param name="experiment_design" value="Test experiment design description"/> @@ -685,7 +703,7 @@ <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"/> + <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/> </repeat> </repeat> </repeat> @@ -696,25 +714,22 @@ <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="--data '1.fastqsanger.gz' '2.fastqsanger.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"> + <test expect_failure="false"> <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" /> + <param name="dry_run" value="true" /> </section> <param name="test_submit" value="True"/> <conditional name="input_format_conditional"> - <param name="add_extension" value="False"/> + <param name="add_extension" value="false"/> <param name="input_format" value="build_tables"/> <conditional name="conditional_viral_metadata"> <param name="viral_sample" value="true"/> @@ -727,7 +742,7 @@ <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="tax_id" value="2697049"/> <param name="collection_date" value="2020"/> <param name="geo_location_country" value="Belgium"/> <param name="host_common_name" value="Human"/> @@ -766,21 +781,18 @@ <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"> + <test expect_failure="false"> <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" /> + <param name="dry_run" value="true" /> </section> <param name="test_submit" value="True"/> <conditional name="input_format_conditional"> - <param name="add_extension" value="False"/> + <param name="add_extension" value="fasle"/> <param name="input_format" value="build_tables"/> <conditional name="conditional_viral_metadata"> <param name="viral_sample" value="True"/> @@ -793,7 +805,7 @@ <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="tax_id" value="2697049"/> <param name="collection_date" value="2020"/> <param name="geo_location_country" value="Belgium"/> <param name="host_common_name" value="Human"/> @@ -817,7 +829,7 @@ <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"/> + <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/> </repeat> </repeat> </repeat> @@ -828,21 +840,17 @@ <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="--data '1.fastqsanger.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> </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 + It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates ]]></help> <citations> </citations>