Mercurial > repos > iuc > ena_webin_cli
diff ena_webin_cli.xml @ 1:93fac0ae859f draft
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 12:13:19 +0000 |
| parents | c9f87770ba8f |
| children | 361a6693aa25 |
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--- a/ena_webin_cli.xml Tue Aug 05 11:53:57 2025 +0000 +++ b/ena_webin_cli.xml Mon Oct 06 12:13:19 2025 +0000 @@ -1,49 +1,56 @@ <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@">8.1.1</token> + <token name="@TOOL_VERSION@">9.0.1</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">ena-webin-cli</requirement> - <requirement type="package" version="1.76">biopython</requirement> <requirement type="package" version="5.3">pyyaml</requirement> </requirements> + <command detect_errors="exit_code"><![CDATA[ -#if $dry_run == "True": - #set $credentials='./test_fake_path'; +## ----------------------------------------------------------------------------- +## 1) Initialize log and credentials +## ----------------------------------------------------------------------------- + +## Truncate (or create) the Galaxy-captured Webin-CLI log dataset. +: > "$webin_cli_log"; + +## Default path where the <configfile name="credentials"> content will be written. +## In dry-run we override this with a fake file so tests don’t require real creds. +#set $credentials = 'credentials' +#if $dry_run == "true": + #set $credentials = './test_fake_path' touch $credentials; - echo "username:test_user" >> $credentials; - echo "password:test_password" >> $credentials; + echo "username:test_user" >> "$credentials"; + echo "password:test_password" >> "$credentials"; #end if +## 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':' -f2,2`; -if [ "\$webin_id" = "" ]; then - ## No credentials in user defined preferences - ## Fallback to global defined credentials (if exist) - #import os - #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): - credentials_path=\${GALAXY_ENA_SECRETS}; - webin_id=`grep 'username' \$GALAXY_ENA_SECRETS | cut -d':' -f2,2` | sed -e 's/^[[:space:]]*//'`; - password=`grep 'password' \$GALAXY_ENA_SECRETS | cut -d':' -f2,2` | sed -e 's/^[[:space:]]*//'`; - if [ "\$webin_id" = "" ]; then - echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information"; - exit 1; - fi; - #else: - echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information"; - exit 1; - #end if +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':' -f2,2`; fi; +## ----------------------------------------------------------------------------- +## 2) Create a base manifest (fields common to all submissions) +## ----------------------------------------------------------------------------- -## create a manifest base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta) +## Name of the base manifest template (we append more fields later). #set $manifest_base = 'manifest_base.tab' -mkdir manifests; -mkdir fasta; +## Working dirs: per-sample manifests and input sequences. +mkdir -p manifests; +mkdir -p fasta; + +## Write assembly-level fields to the base manifest. echo -e 'ASSEMBLY_TYPE\t$assembly_type' > $manifest_base; echo -e 'COVERAGE\t$coverage' >> $manifest_base; echo -e 'PROGRAM\t$assembly_program' >> $manifest_base; @@ -51,8 +58,16 @@ echo -e 'MINGAPLENGTH\t$min_gap_length' >> $manifest_base; #end if echo -e 'MOLECULETYPE\t$molecule_type' >> $manifest_base; - + +## ----------------------------------------------------------------------------- +## 3) Build per-sample manifests depending on metadata workflow +## ----------------------------------------------------------------------------- + #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 $file.is_of_type('fasta'): @@ -61,78 +76,138 @@ #else: ln -s '$file' './fasta/$file.element_identifier'; #end if + #end for - #end for - ## process the input tables, this creates an intermediate file with information - python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta_files './manifests' $manifest_base >> $webin_cli_log; + ## 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'): - gzip -c $metadata_file_or_form.genome_fasta > consensus.fasta.gz; + #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: - ln -s $metadata_file_or_form.genome_fasta consensus.fasta.gz; + #set $fasta_file_name = $metadata_file_or_form.genome_fasta.element_identifier #end if - echo -e 'FASTA\tconsensus.fasta.gz' >> $generated_manifest; + echo -e 'FASTA\t$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 safely with Cheetah +## ----------------------------------------------------------------------------- + +## Webin-CLI will write receipts/logs under this directory (we later tar it). #set $outputs_dir = 'outputs' -mkdir $outputs_dir; +mkdir -p "$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 +## ----------------------------------------------------------------------------- + #if $metadata_file_or_form.metadata_format == "file": - ## iterate over the list of manifest - fasta generated by the process_input - ## in case of errors, this list is empty - while read line; do - manifest=`echo \$line | cut -d' ' -f1,1`; - echo "Submitting manifest \$manifest" >> $webin_cli_log; - ena-webin-cli - -context genome - -userName "'\$webin_id'" - -password "'\$password'" - -centerName "'\$center_name'" - -manifest \$manifest - -inputDir './fasta' - #if $submit_test == "true": - -test - #end if - #if $dry_run == "true": - -validate - #else: - -submit - #end if - -outputDir $outputs_dir - >> $webin_cli_log; + ## Loop over each manifest written by process_input.py (submit_list.tab). + while IFS= read -r line; do + ## Extract the manifest path (first whitespace-delimited field). + manifest=`echo "\$line" | cut -d' ' -f1`; + + ## Log which manifest we are submitting. + echo "Submitting manifest \$manifest" >> "$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: - ena-webin-cli - #if $submit_test == "true": - -test - #end if - #if $dry_run == "true": - -validate - #else: - -submit - #end if - -context genome - -manifest $generated_manifest - -password "'\$password'" - -userName "'\$webin_id'" - -inputDir "./" - -centerName "'\$center_name'" - -outputDir $outputs_dir - >> $webin_cli_log ; + ## 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 +## ----------------------------------------------------------------------------- + +## 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 = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() @@ -140,9 +215,12 @@ username:$webin_id password:$password #end if + ]]></configfile> - ]]></configfile> - <configfile name="genome_fasta_files"> + <!-- 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": @@ -154,42 +232,67 @@ #end if </configfile> </configfiles> -<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> + + <!-- + 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> - <when value="file"> - <param type="data" format="txt" name="ena_receipt" label="Submission receipt obtained from ENA upload tool"/> - <param name="genome_fasta" type="data" label="Select the consensus sequence assembly files or a collection of them" format="fasta,fasta.gz" multiple="true"/> - </when> - <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" label="Select the consensus sequence assembly file" format="fasta,fasta.gz"/> - </when> - </conditional> - <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)"/> + <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/"/> @@ -198,7 +301,9 @@ <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" /> @@ -219,11 +324,57 @@ <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> - <has_n_lines n="4"/> - <has_text_matching expression="ERROR: Invalid submission account user name or password."/> + <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="PRJEB49173"/> + <param name="sample_accession" value="SAMEA11953908"/> + <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" /> @@ -233,7 +384,7 @@ <param name="coverage" value="10000"/> <conditional name="metadata_file_or_form"> <param name="metadata_format" value="file"/> - <param name="ena_receipt" value="receipt_sample_noPhiX.txt"/> + <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"/> @@ -242,11 +393,22 @@ <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."/> + <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$"/> + <has_text_matching expression="(?m)^CHROMOSOME_LIST\t" negate="true"/> + <has_text_matching expression="(?m)^AGP\t" negate="true"/> + </assert_contents> + </element> + </output_collection> </test> + + <!-- Test 4: FILE workflow, single FASTA with metadata --> <test> <param name="submit_test" value="true" /> <param name="dry_run" value="true" /> @@ -262,18 +424,95 @@ <param name="min_gap_length" value="30"/> <output name="webin_cli_log"> <assert_contents> - <has_text_matching expression="ERROR: Invalid submission account user name or password. Please try enclosing your password in single quotes."/> + <has_text_matching expression="Processing sample_alias_001"/> + <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> </assert_contents> </output> </test> + + <!-- Test 5: FILE workflow, AGP for phiX2 --> + <test> + <param name="submit_test" value="true" /> + <param name="dry_run" value="true" /> + <param name="assembly_type" value="isolate"/> + <param name="assembly_program" value="Test assembly program"/> + <param name="molecule_type" value="genomic DNA"/> + <param name="coverage" value="10000"/> + <conditional name="metadata_file_or_form"> + <param name="metadata_format" value="file"/> + <param name="ena_receipt" value="receipt_sample.txt"/> + <param name="genome_fasta" value="phiX2.fasta"/> + <param name="agp_file" value="phiX2.agp"/> + </conditional> + <param name="min_gap_length" value="30"/> + <output name="webin_cli_log"> + <assert_contents> + <has_text_matching expression="Processing phiX2"/> + <has_text_matching expression="ERROR: Invalid submission account user name or password\. Please try enclosing your password in single quotes\."/> + </assert_contents> + </output> + <output_collection name="generated_manifests"> + <element name="phiX2.manifest"> + <assert_contents> + <has_text_matching expression="(?m)^FASTA\tphiX2\.fasta\.gz$"/> + <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> \ No newline at end of file +</tool>