--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ena_webin_cli.xml	Tue Aug 05 11:53:57 2025 +0000
@@ -0,0 +1,279 @@
+<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>
\ No newline at end of file