Mercurial > repos > ieguinoa > ena_upload
diff ena_upload.xml @ 2:2f7a70c0d3ab draft default tip
Uploaded
| author | ieguinoa |
|---|---|
| date | Mon, 21 Feb 2022 14:22:53 +0000 |
| parents | 5d59238cd3f4 |
| children |
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--- a/ena_upload.xml Wed Feb 02 17:30:12 2022 +0000 +++ b/ena_upload.xml Mon Feb 21 14:22:53 2022 +0000 @@ -26,6 +26,10 @@ #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 == "build_tables": @@ -65,13 +69,6 @@ fi; #end if -#if $action_options.test_submit == "True" or $action_options.test_submit_parameters.dry_run == "true": - credentials_path='test_fake_path'; - #if $action_options.test_submit_parameters.dry_run == "true" and $action_options.input_format_conditional.input_format == "excel_tables": - echo "username: test_user" > \$credentials_path; - echo "password: test_password" >> \$credentials_path; - #end if -#end if ## create the list of files to upload and make the symlinks #import re @@ -173,8 +170,6 @@ #end if #end if - -#if $action_options.test_submit_parameters.dry_run == "false" or $action_options.input_format_conditional.input_format == "excel_tables": #if $action_options.action == "add": ena-upload-cli --tool 'ena-upload-cli v@VERSION@ @ Galaxy' @@ -215,6 +210,8 @@ >> '$output'; #end if + + #if $action_options.action == "modify": ena-upload-cli --tool 'ena-upload-cli v@VERSION@ @ Galaxy' @@ -251,27 +248,28 @@ #end if >> '$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 == "build_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 - ## 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; - #end if -#else: - exit 0; + +#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'; +#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[ @@ -453,6 +451,15 @@ <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> <!--Test 3: excel input of NON-VIRAL samples--> <test> @@ -549,7 +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"> @@ -561,7 +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"/> @@ -574,7 +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> @@ -632,7 +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"/> @@ -660,16 +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"/> @@ -682,7 +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"/> @@ -696,7 +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> @@ -707,25 +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"/> @@ -738,7 +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"/> @@ -777,21 +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"/> @@ -804,7 +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"/> @@ -828,7 +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> @@ -839,21 +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>