Mercurial > repos > iuc > ena_upload
diff ena_upload.xml @ 2:9e2df763086c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
author | iuc |
---|---|
date | Thu, 15 Jul 2021 20:12:34 +0000 |
parents | 57251c760cab |
children | 59bb6d34fca6 |
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--- a/ena_upload.xml Fri Apr 30 12:09:25 2021 +0000 +++ b/ena_upload.xml Thu Jul 15 20:12:34 2021 +0000 @@ -1,6 +1,6 @@ -<tool id="ena_upload" name="ENA Upload tool" version="0.3.1" profile="20.01" license="MIT"> +<tool id="ena_upload" name="ENA Upload tool" version="0.3.2" profile="20.01" license="MIT"> <macros> - <token name="@VERSION@">0.2.7</token> + <token name="@VERSION@">0.3.1</token> <import>samples_macros.xml</import> </macros> <requirements> @@ -48,7 +48,6 @@ ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && #end if - #if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False": webin_id=`grep 'username' $credentials`; if [ "\$webin_id" = "" ]; then @@ -292,7 +291,58 @@ <assert_contents> <has_n_lines n="5"/> <has_n_columns n="18"/> - <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tcollection_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tsubmission_date"/> + <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date"/> + </assert_contents> + </output> + <output name="runs_table_out"> + <assert_contents> + <has_n_lines n="5"/> + <has_n_columns n="8"/> + <has_line_matching expression="alias\tstatus\taccession\texperiment_alias\tfile_name\tfile_format\tfile_checksum\tsubmission_date"/> + <has_line_matching expression="r_(.*)_026\tadd\tena_run_accession\te_(.*)_026\tC026_exp5_clean.fastq.gz\tfastq\tfile_checksum\tsubmission_date_ENA"/> + </assert_contents> + </output> + </test> + <!--Test excel input of VIRAL samples with extended columns--> + <test> + <conditional name="action_options"> + <param name="action" value="add"/> + <section name="test_submit_parameters"> + <param name="submit_dev" value="false" /> + <param name="dry_run" value="true" /> + </section> + <conditional name="input_format_conditional"> + <param name="input_format" value="excel_tables"/> + <param name="viral_submission" value="True"/> + <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/> + <conditional name="run_input_format_conditional"> + <param name="run_input_format" value="multiple_selection_list"/> + <param name="data" value="sample.fq"/> + </conditional> + </conditional> + </conditional> + <param name="center" value="Some research center"/> + <output name="experiments_table_out"> + <assert_contents> + <has_n_lines n="5"/> + <has_n_columns n="17"/> + <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\tsubmission_date" /> + <has_line_matching expression="e_(.*)_026\tadd\taccession_ena\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> + </assert_contents> + </output> + <output name="studies_table_out"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="8"/> + <has_line_matching expression="alias\tstatus\taccession\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\tsubmission_date"/> + <has_line_matching expression="SARS-CoV-2_genomes_01\tadd\tENA_accession\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> + </assert_contents> + </output> + <output name="samples_table_out"> + <assert_contents> + <has_n_lines n="5"/> + <has_n_columns n="42"/> + <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date\tgeographic_location\thost_common_name\thost_subject_id\thost_health_state\thost_sex\thost_scientific_name\tcollector_name\tcollecting_institution\tisolate\tcollection_date\tgeographic_location_latitude\tgeographic_location_longitude\tsample_capture_status\thost_disease_outcome\thost_age\tvirus_identifier\treceipt_date\tdefinition_for_seropositive_sample\tserotype\thost_habitat\tisolation_source_host_associated\thost_behaviour\tisolation_source_non_host_associated\tsubject_exposure\tsubject_exposure_duration\ttype_exposure\tpersonal_protective_equipment\thospitalisation\tillness_duration\tillness_symptoms\tsample_storage_conditions\tstrain\thost_description\tgravidity"/> </assert_contents> </output> <output name="runs_table_out"> @@ -341,7 +391,7 @@ <assert_contents> <has_n_lines n="5"/> <has_n_columns n="8"/> - <has_line_matching expression="alias\tstatus\taccession\ttitle\tscientific_name\ttaxon_id\tsample_description\tsubmission_date"/> + <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\tstatus\taccession\ttaxon_id\tsubmission_date"/> </assert_contents> </output> <output name="runs_table_out"> @@ -628,7 +678,7 @@ This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables It is also possible to submit an excel file by following the template in https://drive.google.com/file/d/1ncC22--tW2v-EI-te_r86sAZujIPAjlX/view?usp=sharing - For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1U4VdcczsIecIXxseV8svE1zO_CBUadog/view?usp=sharing + For viral submissions a larger set of metadata is required, you can find the template in https://drive.google.com/file/d/1Gx78GKh58PmRjdmJ05DBbpObAL-3oUFX/view?usp=sharing ]]></help> <citations> </citations>