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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 6f9ce1aba91681e831f2649fb36b74cc3d572eb3
| author | iuc |
|---|---|
| date | Fri, 24 Oct 2025 08:03:03 +0000 |
| parents | 7f669682f4ac |
| children |
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<tool id="ena_webin_cli" name="ENA Webin CLI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="24.2"> <description>Submission of consensus sequences to the European Nucleotide Archive (ENA)</description> <macros> <token name="@TOOL_VERSION@">9.0.1</token> <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">ena-webin-cli</requirement> <requirement type="package" version="5.3">pyyaml</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## ----------------------------------------------------------------------------- ## 1) Initialize log and credentials ## ----------------------------------------------------------------------------- echo "Initializing log and credentials"; ## Truncate (or create) the Galaxy-captured Webin-CLI log dataset. : > "$webin_cli_log"; ## Extract username/password from the credentials file. ## NOTE: $webin_id appears in bash, so we escape it as \$webin_id. webin_id=`grep 'username' $credentials | cut -d':' -f2`; if [ -z "\$webin_id" ]; then ## Fail early with guidance if no username is present. echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information" >&2; exit 1; else ## Pull the password similarly. password=`grep 'password' $credentials | cut -d':' -f2`; fi; ## ----------------------------------------------------------------------------- ## 2) Create a base manifest (fields common to all submissions) ## ----------------------------------------------------------------------------- echo "Creating a base manifest (fields common to all submissions)"; ## Name of the base manifest template (we append more fields later). #set $manifest_base = 'manifest_base.tab' ## Working dirs: per-sample manifests and input sequences. mkdir -p manifests; mkdir -p fasta; ## Write assembly-level fields to the base manifest. echo -e 'ASSEMBLY_TYPE\t$assembly_type' > $manifest_base; echo -e 'COVERAGE\t$coverage' >> $manifest_base; echo -e 'PROGRAM\t$assembly_program' >> $manifest_base; #if $min_gap_length: echo -e 'MINGAPLENGTH\t$min_gap_length' >> $manifest_base; #end if echo -e 'MOLECULETYPE\t$molecule_type' >> $manifest_base; ## ----------------------------------------------------------------------------- ## 3) Build per-sample manifests depending on metadata workflow ## ----------------------------------------------------------------------------- echo "Building per-sample manifests depending on metadata workflow"; #if $metadata_file_or_form.metadata_format == "file": ## --------------------------- FILE-DRIVEN WORKFLOW ------------------------ ## For each selected FASTA: ## - if uncompressed (.fasta), gzip it into ./fasta/<name>.fasta.gz ## - if already .fasta.gz, symlink it into ./fasta #import re #for $file in $metadata_file_or_form.genome_fasta: #if $file.is_of_type('fasta'): #set $full_name = $file.element_identifier + '.gz' gzip -c '$file' > './fasta/$full_name'; #else: ln -s '$file' './fasta/$file.element_identifier'; #end if #end for ## Optionally link AGP and chromosome list files if provided (one per sample). #if $metadata_file_or_form.agp_file: #for $file in $metadata_file_or_form.agp_file: ln -s '$file' './fasta/$file.element_identifier'; #end for #end if #if $metadata_file_or_form.chr_list_file: #for $file in $metadata_file_or_form.chr_list_file: #set $chr_name = $file.element_identifier + '.gz' gzip -c '$file' > './fasta/$chr_name'; #end for #end if ## Helper script: ## - parses ENA receipt (study/sample accessions, platform), ## - writes per-sample manifests into ./manifests using $manifest_base, ## - emits "submit_list.tab" (one manifest path per line). python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta_files './manifests' $manifest_base >> "$webin_cli_log" 2>&1; ## Extract center name from the receipt (used as -centerName). center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`; ## Log if submit_list.tab exists, and dump its content for debugging. if [ -s submit_list.tab ]; then echo "submit_list.tab present:" >> "$webin_cli_log" 2>&1; cat submit_list.tab >> "$webin_cli_log" 2>&1; else echo "submit_list.tab is missing or empty" >> "$webin_cli_log" 2>&1; fi; #else: ## --------------------------- FORM-DRIVEN WORKFLOW ------------------------ ## Single-manifest flow: copy base, then append form fields. #set $generated_manifest='./manifests/generated_manifest.txt' cp $manifest_base $generated_manifest; ## Use local Cheetah vars for readability. #set $study_id = $metadata_file_or_form.study_accession #set $sample_id = $metadata_file_or_form.sample_accession ## Required accessions. echo -e 'STUDY\t$study_id' >> $generated_manifest; echo -e 'SAMPLE\t$sample_id' >> $generated_manifest; ## center_name is given by the user in this path. center_name='$metadata_file_or_form.center_name'; ## Assembly name and platform. echo -e 'NAME\t$metadata_file_or_form.assembly_name' >> $generated_manifest; echo -e 'PLATFORM\t$metadata_file_or_form.sequencing_platform' >> $generated_manifest; ## Normalize FASTA name referenced by the manifest. #if $metadata_file_or_form.genome_fasta.is_of_type('fasta'): #set $fasta_file_name = $metadata_file_or_form.genome_fasta.element_identifier + '.gz' gzip -c '$metadata_file_or_form.genome_fasta' > $fasta_file_name; #else: #set $fasta_file_name = $metadata_file_or_form.genome_fasta.element_identifier #end if echo -e 'FASTA\t$fasta_file_name' >> $generated_manifest; ## Optional extras for chromosome-scale assemblies. #if $metadata_file_or_form.agp_file: echo -e 'AGP\t$metadata_file_or_form.agp_file.element_identifier' >> $generated_manifest; #end if #if $metadata_file_or_form.chr_list_file: ## If the name ends with .tsv, gzip it and reference the .gz; else use as-is. #set $chr_file_name = $metadata_file_or_form.chr_list_file.element_identifier + '.gz' gzip -c '$metadata_file_or_form.chr_list_file' > $chr_file_name; echo -e 'CHROMOSOME_LIST\t$chr_file_name' >> $generated_manifest; #end if #end if ## ----------------------------------------------------------------------------- ## 4) Prepare output directory and build CLI flags ## ----------------------------------------------------------------------------- echo "Preparing output directory and build CLI flags"; ## Webin-CLI will write receipts/logs under this directory (we later tar it). #set $outputs_dir = 'outputs' mkdir -p "$outputs_dir"; ## Build flags using #set (safer than inline #if within a single shell line). #set $test_flag = '' #if $submit_test == "true": #set $test_flag = ' -test' #end if ## By default we submit; in dry_run we validate instead. #set $action_flag = ' -submit' #if $dry_run == "true": #set $action_flag = ' -validate' #end if ## ----------------------------------------------------------------------------- ## 5) Execute Webin-CLI ## ----------------------------------------------------------------------------- echo "Executing Webin-CLI"; #if $metadata_file_or_form.metadata_format == "file": ## Loop over each manifest written by process_input.py (submit_list.tab). while IFS= read -r line; do ## Extract the manifest path (first whitespace-delimited field). manifest=`echo "\$line" | cut -d' ' -f1`; ## Log which manifest we are submitting. echo "Submitting manifest \$manifest" >> "$webin_cli_log" 2>&1; ## Invoke Webin-CLI with computed flags. ena-webin-cli -context genome -manifest "\$manifest" -userName "\$webin_id" -password "\$password" -centerName "\$center_name" -inputDir "./fasta" $test_flag $action_flag -outputDir $outputs_dir >> '$webin_cli_log' 2>&1 || true; done < submit_list.tab; #else: ## Single run in "form" mode with the one generated manifest. ena-webin-cli -context genome -manifest $generated_manifest -userName "\$webin_id" -password "\$password" -centerName "\$center_name" -inputDir "./" $test_flag $action_flag -outputDir $outputs_dir >> "$webin_cli_log" 2>&1 || true; #end if ## ----------------------------------------------------------------------------- ## 6) Package outputs for Galaxy ## ----------------------------------------------------------------------------- echo "Packaging outputs for Galaxy"; ## Tar up the Webin-CLI output directory so Galaxy can collect a single dataset. tar -cf $webin_cli_outputs $outputs_dir ; ]]></command> <!-- Config files rendered by Galaxy *before* the command runs. They are plain text files placed in the job working directory and referenced above. --> <configfiles> <!-- Credentials file: Pulls stored ENA Webin details (if set) from the Galaxy user preferences and writes simple "username:..." and "password:..." lines. The command reads from this file. --> <configfile name="credentials"><![CDATA[ #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip() #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() ## In dry-run we add fake creds when not provided. #if $webin_id == "" and $dry_run == "true": #set $webin_id = "test-webin" #set $password = "test-password" #end if #if $webin_id != "" : username:$webin_id password:$password #end if ]]></configfile> <!-- genome_fasta_files: In "file" mode, build a JSON array containing the *element_identifier* (dataset name) for each selected FASTA. process_input.py uses these names to derive sample aliases. --> <configfile name="genome_fasta_files"> #import json #import re #if $metadata_file_or_form.metadata_format == "file": #set $fasta_files_list = list() #for $file in $metadata_file_or_form.genome_fasta: $fasta_files_list.append(str($file.element_identifier)) #end for #echo json.dumps($fasta_files_list) #end if </configfile> </configfiles> <!-- User-facing inputs: - Assembly-level parameters - Choice of metadata workflow (file vs form) with corresponding fields - Submission toggles for ENA test server and validation-only --> <inputs> <param name="assembly_type" type="select" label="Assembly type"> <option value="clone">Clone</option> <option value="isolate">Isolate</option> <option value="COVID-19 outbreak">COVID-19 outbreak</option> </param> <param name="assembly_program" type="text" optional="False" label="Assembly program"/> <param name="molecule_type" type="select" label="Molecule type"> <option value="genomic RNA" selected="True">genomic RNA</option> <option value="viral cRNA">viral cRNA</option> <option value="genomic DNA">genomic DNA</option> </param> <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/> <param name="min_gap_length" type="text" optional="True" label="Minimum gap length (optional)"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" type="select" label="Select the method to load study and sample metadata"> <option value="form" selected="True">Fill in required submission metadata</option> <option value="file">I used the Galaxy ENA upload tool to submit the raw data: parse the received submission receipt</option> </param> <!-- FILE workflow: receipt + multiple FASTA (+ optional AGP/TSV) --> <when value="file"> <param type="data" format="txt" name="ena_receipt" optional="False" label="Submission receipt obtained from ENA upload tool"/> <param name="genome_fasta" type="data" optional="False" label="Select the consensus sequence assembly files or a collection of them. Use following syntax: sample_alias.fasta or sample_alias.fasta.gz" format="fasta,fasta.gz" multiple="true"/> <param name="agp_file" type="data" optional="True" label="Sequences in AGP format. Use following syntax: sample_alias.agp" format="agp" multiple="true"/> <param name="chr_list_file" type="data" optional="True" label="Chromosome List File, must be provided when the submission contains assembled chromosomes. Use following syntax: sample_alias.tsv" format="tsv" multiple="true"/> </when> <!-- FORM workflow: single, user-specified submission --> <when value="form"> <param name="assembly_name" type="text" optional="False" label="Assembly name"/> <param name="study_accession" type="text" optional="False" label="Study accession"/> <param name="sample_accession" type="text" optional="False" label="Sample accession"/> <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/> <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/> <param name="center_name" type="text" optional="False" label="Center name"/> <param name="genome_fasta" type="data" optional="False" label="Select the consensus sequence assembly file" format="fasta,fasta.gz"/> <param name="agp_file" type="data" optional="True" label="Sequences in AGP format." format="agp"/> <param name="chr_list_file" type="data" optional="True" label="Chromosome List File, must be provided when the submission contains assembled chromosomes." format="tsv"/> </when> </conditional> <!-- Submission controls --> <param name="submit_test" type="boolean" truevalue="true" falsevalue="false" label="Submit to ENA test server" help="Uploads to the test server of ENA will not be made public and will be removed automatically in 24 hours. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find these uploads at https://wwwdev.ebi.ac.uk/ena/." /> <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Validate files and metadata but do not submit" help="Generate input files and run Webin-CLI with -validate option. If 'No' is selected then it will validate and submit (-submit flag)"/> </inputs> <!-- Outputs: - generated_manifests: discovered in manifests/ (via regex) for transparency - webin_cli_log: combined stdout/stderr + helper echo statements - webin_cli_outputs: tar archive of the Webin-CLI output directory --> <outputs> <collection name="generated_manifests" type="list" label="Generated manifests"> <discover_datasets pattern="(?P<designation>.+)\.txt" ext="txt" directory="manifests/"/> </collection> <data name="webin_cli_log" label="ENA submission log" format="txt"/> <data name="webin_cli_outputs" label="Webin cli outputs" format="tar"/> </outputs> <tests> <!-- Test 1: FORM workflow, no chr/AGP --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="viral cRNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="form"/> <param name="assembly_name" value="Test assembly name"/> <param name="study_accession" value="FAKE001"/> <param name="sample_accession" value="FAKESAMP001"/> <param name="sequencing_platform" value="Nanopore 0011"/> <param name="description" value="Test Description"/> <param name="center_name" value="Test center name"/> <param name="genome_fasta" value="phiX2.fasta"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="ERROR: Invalid submission account user name or password\."/> </assert_contents> </output> <output_collection name="generated_manifests"> <element name="generated_manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/> <has_text_matching expression="(?m)^AGP\t" negate="true"/> </assert_contents> </element> </output_collection> </test> <!-- Test 2: FORM workflow, chr list present --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="genomic DNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="form"/> <param name="assembly_name" value="Test assembly name"/> <param name="study_accession" value="FAKE001"/> <param name="sample_accession" value="FAKESAMP001"/> <param name="sequencing_platform" value="Nanopore 0011"/> <param name="description" value="Test Description"/> <param name="center_name" value="Test center name"/> <param name="genome_fasta" value="phiX3.fasta"/> <param name="chr_list_file" value="phiX3.tsv"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="ERROR: Invalid submission account user name or password\."/> </assert_contents> </output> <output_collection name="generated_manifests"> <element name="generated_manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tphiX3\.fasta\.gz$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\tphiX3\.tsv\.gz$"/> <has_text_matching expression="(?m)^AGP\t" negate="true"/> </assert_contents> </element> </output_collection> </test> <!-- Test 3: FILE workflow, two FASTAs; one missing metadata --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="viral cRNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="file"/> <param name="ena_receipt" value="receipt_sample_nophiX2.txt"/> <param name="genome_fasta" value="phiX2.fasta.gz,sample_alias_001.fasta.gz"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="Processing phiX2"/> <has_text_matching expression="No metadata found for sample phiX2"/> <has_text_matching expression="Processing sample_alias_001"/> <has_text_matching expression="Submitting manifest .*manifests/sample_alias_001\.manifest\.txt"/> <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> </assert_contents> </output> <output_collection name="generated_manifests"> <element name="sample_alias_001.manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tsample_alias_001\.fasta\.gz$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/> <has_text_matching expression="(?m)^AGP\t" negate="true"/> </assert_contents> </element> </output_collection> </test> <!-- Test 4: FILE workflow, single FASTA with metadata --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="viral cRNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="file"/> <param name="ena_receipt" value="receipt_sample.txt"/> <param name="genome_fasta" value="sample_alias_001.fasta.gz"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="Processing sample_alias_001"/> <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> </assert_contents> </output> </test> <!-- Test 5: FILE workflow, AGP for phiX2 --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="genomic DNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="file"/> <param name="ena_receipt" value="receipt_sample.txt"/> <param name="genome_fasta" value="phiX2.fasta"/> <param name="agp_file" value="phiX2.agp"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="Processing phiX2"/> <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> </assert_contents> </output> <output_collection name="generated_manifests"> <element name="phiX2.manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/> <has_text_matching expression="(?m)^AGP\tphiX2\.agp$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/> </assert_contents> </element> </output_collection> </test> <!-- Test 6: FILE workflow, chr list for phiX3 + extra fasta --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> <param name="assembly_type" value="isolate"/> <param name="assembly_program" value="Test assembly program"/> <param name="molecule_type" value="genomic DNA"/> <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="file"/> <param name="ena_receipt" value="receipt_sample_phiX3.txt"/> <param name="genome_fasta" value="phiX3.fasta,phiX2.fasta.gz"/> <param name="chr_list_file" value="phiX3.tsv"/> </conditional> <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> <has_text_matching expression="Processing phiX3"/> <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> </assert_contents> </output> <output_collection name="generated_manifests"> <element name="phiX2.manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/> <has_text_matching expression="(?m)^AGP\t" negate="true"/> </assert_contents> </element> <element name="phiX3.manifest"> <assert_contents> <has_text_matching expression="(?m)^FASTA\tphiX3\.fasta\.gz$"/> <has_text_matching expression="(?m)^CHROMOSOME_LIST\tphiX3\.tsv\.gz$"/> <has_text_matching expression="(?m)^AGP\t" negate="true"/> </assert_contents> </element> </output_collection> </test> </tests> <!-- Help text + citation --> <help><![CDATA[ This tool is a wrapper for the ENA Webin CLI submission tool (https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html). .. class:: warningmark The ENA upload tool won't work unless you have provided an ENA Webin ID in User > Preferences > Manage Information > ENA Webin account details.]]></help> <citations> <citation type="doi">10.1093/nar/gkac1051</citation> </citations> </tool>