--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datasets_genome.xml	Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,215 @@
+<tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE" version="@TOOL_VERSION@">
+    <description>download genome sequence, annotation and metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"></expand>
+    <command><![CDATA[
+@SETUP_CERTIFICATES@
+datasets download genome $query.subcommand.download_by
+#if $query.subcommand.download_by == 'accession':
+    #if $query.subcommand.text_or_file.text_or_file == 'text':
+        #echo " ".join(f"'{x}'" for x in $query.subcommand.text_or_file.accession.split(' ') if x)
+    #else
+        --inputfile '$query.subcommand.text_or_file.inputfile'
+    #end if
+#else:
+    '$query.subcommand.taxon'
+#end if
+$filters.reference
+$filters.annotated
+#if $filters.assembly_level:
+--assembly_level $filters.assembly_level
+#end if
+#if $filters.assembly_source:
+--assembly_source $filters.assembly_source
+#end if
+#if $filters.chromosomes:
+--chromosomes '$filters.chromosomes'
+#end if
+@EXCLUDES_GENOME@
+@INCLUDES_GENOME@
+@RELEASED_BEFORE@
+@RELEASED_SINCE@
+#for search_term in $filters.search:
+    --search '$filters.search_term'
+#end for
+#if $uncompressed
+&& unzip ncbi_dataset.zip
+#else
+&& unzip -l ncbi_dataset.zip > ncbi_dataset.txt
+#end if
+]]></command>
+    <inputs>
+        <section name="query" title="Query" expanded="true">
+            <conditional name="subcommand">
+                <param name="download_by" type="select" label="Choose how to find genomes to download">
+                    <option value="accession">Download by NCBI assembly or BioProject accession</option>
+                    <option value="taxon">Download by taxon</option>
+                </param>
+                <when value="accession">
+                    <expand macro="text_or_file"/>
+                </when>
+                <when value="taxon">
+                    <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."></param>
+                </when>
+            </conditional>
+        </section>
+        <section name="filters" title="Filters and Limit">
+            <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>            
+            <expand macro="annotation"></expand>
+            <expand macro="assembly_level"></expand>
+            <expand macro="assembly_source"></expand>
+            <expand macro="chromosomes"></expand>
+            <expand macro="released_options"></expand>
+            <expand macro="released_options" before_or_after="since"></expand>
+
+            <repeat name="search" title="Add search terms">
+                <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/>
+            </repeat>
+        </section>
+        <section name="file_choices" title="File Choices">
+            <expand macro="excludes_genome"></expand>
+            <expand macro="includes_genome"></expand>
+        </section>
+        <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/>
+    </inputs>
+    <outputs>
+        <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip">
+            <filter>not uncompressed</filter>
+        </data>
+        <data name="archive_contents" format="txt" label="Archive Contents" from_work_dir="ncbi_dataset.txt">
+            <filter>not uncompressed</filter>
+        </data>
+        <data name="genome_data_report" format="json" label="NCBI Genome Datasets: Data Report" from_work_dir="ncbi_dataset/data/assembly_data_report.jsonl">
+            <filter>uncompressed</filter>
+        </data>
+        <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed</filter>
+        </collection>
+        <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/.*(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['exclude_seq']</filter>
+        </collection>
+        <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['exclude_genomic_cds']</filter>
+        </collection>
+        <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['exclude_gff3']</filter>
+        </collection>
+        <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['exclude_rna']</filter>
+        </collection>
+        <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['exclude_protein']</filter>
+        </collection>
+        <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['include_gbff']</filter>
+        </collection>
+        <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <filter>uncompressed and file_choices['include_gtf']</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="taxon"></param>
+                <param name="text_or_file" value="text"></param>
+                <param name="taxon" value="human"></param>
+            </conditional>
+            <param name="chromosomes" value="21"></param>
+            <param name="uncompressed" value="false"/>
+            <param name="released_before" value="01/01/2018"></param>
+            <output name="archive_contents">
+                <assert_contents>
+                    <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="5">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="accession"></param>
+                <conditional name="text_or_file">
+                    <param name="text_or_file" value="text"></param>
+                    <param name="accession" value="GCF_000013305.1 GCF_000007445.1"></param>
+                </conditional>
+            </conditional>
+            <param name="uncompressed" value="true"/>
+            <param name="released_before" value="01/01/2007"></param>
+            <param name="exclude_genomic_cds" value="true"/>
+            <param name="include_gtf" value="true"/>
+            <output name="genome_data_report">
+                <assert_contents>
+                    <has_text text="GCF_000013305.1"/>
+                </assert_contents>
+            </output>
+            <output_collection name="sequence_report" type="list">
+                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
+                <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
+            </output_collection>
+            <output_collection name="genomic_gtf" type="list">
+                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
+                <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
+            </output_collection>
+            <output_collection name="genomic_cds" type="list">
+                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
+                <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="4">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="accession"></param>
+                <conditional name="text_or_file">
+                    <param name="text_or_file" value="file"></param>
+                    <param name="inputfile" value="accessions.txt"></param>
+                </conditional>
+            </conditional>
+            <param name="include_gbff" value="true"/>
+            <param name="exclude_seq" value="false"/>
+            <param name="exclude_gff3" value="true"/>
+            <param name="uncompressed" value="true"/>
+            <param name="released_before" value="01/02/2007"></param>
+            <output name="genome_data_report">
+                <assert_contents>
+                   <has_text text="SAMN02604181"/>
+                </assert_contents>
+            </output>
+            <output_collection name="sequence_report" type="list">
+                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
+                <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
+            </output_collection>
+            <output_collection name="genomic_gff" type="list">
+                <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
+                <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
+            </output_collection>
+            <output_collection name="genomic_gbff" type="list">
+                <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
+                <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**Download Genome Datasets from NCBI**
+
+Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
+Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
+
+Tthe default genome dataset includes the following files (if available):
+ * genomic.fna (genomic sequences)
+ * rna.fna (transcript sequences)
+ * protein.faa (protein sequences)
+ * genomic.gff (genome annotation in gff3 format)
+ * data_report.jsonl (data report with genome assembly and annotation metadata)
+ * dataset_catalog.json (a list of files and file types included in the dataset)
+]]>
+    </help>
+
+</tool>