Mercurial > repos > iuc > ena_webin_cli

diff test-data/receipt_sample.txt @ 0:7f669682f4ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
author iuc
date Mon, 06 Oct 2025 12:13:07 +0000
parents
children 1090ae5e7b29
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/receipt_sample.txt	Mon Oct 06 12:13:07 2025 +0000
@@ -0,0 +1,76 @@
+YAML -------------
+ENA_experiment:
+  0:
+    alias: exp_test_alias_001
+    design_description: Lot's of coffe and magic
+    insert_size: 250.0
+    instrument_model: NextSeq 500
+    library_construction_protocol: Illumina COVIDSeq Test Kit
+    library_layout: PAIRED
+    library_name: Cov51
+    library_selection: RT-PCR
+    library_source: VIRAL RNA
+    library_strategy: AMPLICON
+    platform: ILLUMINA
+    sample_alias: sample_alias_001
+    study_alias: study_alias_001
+    title: Illumina NextSeq paired end sequencing; Illumina COVIDSeq Test
+  1:
+    alias: exp_test_alias_002
+    design_description: Lot's of coffe and magic
+    insert_size: 250.0
+    instrument_model: NextSeq 500
+    library_construction_protocol: Illumina COVIDSeq Test Kit
+    library_layout: PAIRED
+    library_name: Cov51
+    library_selection: RT-PCR
+    library_source: VIRAL RNA
+    library_strategy: AMPLICON
+    platform: ILLUMINA
+    sample_alias: phiX2
+    study_alias: study_alias_001
+    title: Illumina NextSeq paired end sequencing; Illumina COVIDSeq Test
+ENA_run:
+  2:
+    alias: run_alias_001
+    experiment_alias: exp_test_alias_001
+    file_format: FASTQ
+    file_name: run001.fastq.gz
+ENA_sample:
+  2:
+    alias: sample_alias_001
+    collecting institution: Umbrella Corp.
+    collection date: '2021-05-03'
+    collector name: "John Doe"
+    definition for seropositive sample: ''
+  2:
+    alias: phiX2
+    collecting institution: Umbrella Corp.
+    collection date: '2021-05-03'
+    collector name: "John Doe"
+    definition for seropositive sample: ''
+ENA_study:
+  2:
+    alias: study_alias_001
+    study_abstract: "Help"
+    study_type: Whole Genome Sequencing
+    title: Whole genome sequencing of SARS-CoV-2
+YAML -------------
+
+Printing receipt to ./receipt.xml
+
+Submission was done successfully
+
+Study accession details:
+study_alias_001	FAKE0001	2011-01-16T10:52:06.497+01:00	added
+
+Sample accession details:
+sample_alias_001	FAKESAMP001	2011-01-16T10:52:06.497+01:00	added
+phiX2	FAKESAMP002	2011-01-16T10:52:06.497+01:00	added
+
+Saving updates in new tsv tables::
+save updates in ./submission_files/studies_updated.tsv
+save updates in ./submission_files/samples_updated.tsv
+save updates in ./submission_files/experiments_updated.tsv
+save updates in ./submission_files/runs_updated.tsv
+action_option	add