<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="@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';
    touch $credentials;
    echo "username:test_user" >> $credentials;
    echo "password:test_password" >> $credentials;
#end if

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
else
  password=`grep 'password' $credentials | cut -d':' -f2,2`;
fi;


## create a manifest base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)
#set $manifest_base = 'manifest_base.tab'
mkdir manifests;
mkdir fasta;

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;
        
#if $metadata_file_or_form.metadata_format == "file":
    #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
    ## 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;
    center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`;
#else:
    #set $generated_manifest='./manifests/generated_manifest.txt'
    cp $manifest_base $generated_manifest;
    #set $study_id = $metadata_file_or_form.study_accession
    #set $sample_id = $metadata_file_or_form.sample_accession
    echo -e 'STUDY\t$study_id' >> $generated_manifest;
    echo -e 'SAMPLE\t$sample_id' >> $generated_manifest;
    center_name='$metadata_file_or_form.center_name';
    echo -e 'NAME\t$metadata_file_or_form.assembly_name' >> $generated_manifest;
    echo -e 'PLATFORM\t$metadata_file_or_form.sequencing_platform' >> $generated_manifest;
    #if $metadata_file_or_form.genome_fasta.is_of_type('fasta'):
        gzip -c $metadata_file_or_form.genome_fasta > consensus.fasta.gz;
    #else:
        ln -s $metadata_file_or_form.genome_fasta consensus.fasta.gz;
    #end if
    echo -e 'FASTA\tconsensus.fasta.gz' >> $generated_manifest;
#end if

#set $outputs_dir = 'outputs'
mkdir $outputs_dir;
#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;
    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 ;
#end if
tar -cf $webin_cli_outputs $outputs_dir ;
]]></command>
    <configfiles>
        <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()
#if $webin_id != "":
    username:$webin_id
    password:$password
#end if

        ]]></configfile>
    <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>
<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>
        <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)"/>
    </inputs>
    <outputs>
        <collection name="generated_manifests" type="list" label="Generated manifests">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.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>
            <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="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="phiX2.fasta"/>
            </conditional>
            <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."/>
                </assert_contents>
            </output>
        </test>
        <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_noPhiX.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>
        </test>
        <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="ERROR: Invalid submission account user name or password. Please try enclosing your password in single quotes."/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <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>