--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aws_sra.xml	Mon Mar 23 14:09:35 2026 +0000
@@ -0,0 +1,360 @@
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.1" profile="23.0">
+    <description>Fetch SRA data files from NCBI's public AWS S3 buckets</description>
+
+    <requirements>
+        <requirement type="package" version="2.34.8" channel="conda-forge">awscli</requirement>
+        <requirement type="package" version="3.2.1" channel="bioconda">sra-tools</requirement>
+        <requirement type="package" version="2.8" channel="conda-forge">pigz</requirement>
+    </requirements>
+
+    <version_command>aws --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+        ## ── Resolve bucket base URL ──────────────────────────────────────────────
+        #if $source.bucket == 'sra_pub_run_odp'
+            #set $s3_base = 's3://sra-pub-run-odp'
+        #elif $source.bucket == 'sra_pub_src_1'
+            #set $s3_base = 's3://sra-pub-src-1'
+        #elif $source.bucket == 'sra_pub_src_2'
+            #set $s3_base = 's3://sra-pub-src-2'
+        #elif $source.bucket == 'sra_pub_metadata'
+            #set $s3_base = 's3://sra-pub-metadata-us-east-1/sra/metadata'
+        #end if
+
+        ## ── LIST mode ────────────────────────────────────────────────────────────
+        #if $action.mode == 'list'
+            aws s3 ls
+                --no-sign-request
+                #if $source.prefix
+                    '${s3_base}/${ $source.prefix.strip("/") }/'
+                #else
+                    '${s3_base}/'
+                #end if
+                #if $action.recursive
+                    --recursive
+                #end if
+            > '$output_list'
+
+        ## ── DOWNLOAD RAW mode ────────────────────────────────────────────────────
+        #elif $action.mode == 'copy'
+            aws s3 cp
+                --no-sign-request
+                #if $action.recursive
+                    --recursive
+                #end if
+                '${s3_base}/${ $action.s3_key.strip("/") }'
+                '$output_data'
+
+        ## ── FASTQ DUMP mode (sra-pub-run-odp only) ───────────────────────────────
+        #elif $action.mode == 'fastq_dump'
+            #set $acc = $action.accession.strip()
+
+            ## 1. Download the .sra file from S3
+            mkdir -p sra_cache &&
+            aws s3 cp
+                --no-sign-request
+                '${s3_base}/sra/${acc}/${acc}.sra'
+                ./sra_cache/${acc}.sra &&
+
+            ## 2. Convert with fasterq-dump --split-files.
+            ##    Paired runs  → <acc>_1.fastq + <acc>_2.fastq
+            ##    Single runs  → <acc>.fastq   (no _1/_2 suffix)
+            ##    We always use --split-files; single-end runs simply produce one file.
+            mkdir -p fastq_out &&
+            fasterq-dump
+                ./sra_cache/${acc}.sra
+                --outdir ./fastq_out
+                --temp .
+                --threads \${GALAXY_SLOTS:-4}
+                --split-files
+            &&
+
+            ## 3. Compress with pigz (fasterq-dump does not gzip natively)
+            pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
+
+            ## 4. Stage outputs
+            #if $action.layout == 'paired'
+                cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
+                cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
+            #else
+                cp ./fastq_out/${acc}.fastq.gz '$output_r1'
+            #end if
+        #end if
+    ]]></command>
+
+    <inputs>
+        <section name="source" title="Data Source" expanded="true">
+            <param name="bucket" type="select" label="SRA S3 Bucket"
+                   help="Select the NCBI SRA AWS Open Data bucket to access. FASTQ conversion is only available for sra-pub-run-odp.">
+                <option value="sra_pub_run_odp" selected="true">
+                    sra-pub-run-odp — Open-access SRA runs (.sra format)
+                </option>
+                <option value="sra_pub_src_1">
+                    sra-pub-src-1 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 1]
+                </option>
+                <option value="sra_pub_src_2">
+                    sra-pub-src-2 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 2]
+                </option>
+                <option value="sra_pub_metadata">
+                    sra-pub-metadata-us-east-1 — SRA metadata (Parquet/CSV for Athena/Glue)
+                </option>
+            </param>
+            <param name="prefix" type="text" value="" optional="true"
+                   label="S3 key prefix (optional)"
+                   help="Restrict listing to a sub-path, e.g. 'sra/SRR000001'. Used only in List mode.">
+                <sanitizer invalid_char="">
+                    <valid initial="string.printable">
+                        <remove value="'"/>
+                        <remove value='"'/>
+                    </valid>
+                </sanitizer>
+            </param>
+        </section>
+
+        <conditional name="action">
+            <param name="mode" type="select" label="Action">
+                <option value="list" selected="true">List objects</option>
+                <option value="copy">Download raw file(s)</option>
+                <option value="fastq_dump">Download and convert to FASTQ (sra-pub-run-odp only)</option>
+            </param>
+
+            <!-- ── LIST ── -->
+            <when value="list">
+                <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
+                       checked="false" label="List recursively"
+                       help="List all objects under the prefix, not just the immediate level."/>
+            </when>
+
+            <!-- ── COPY ── -->
+            <when value="copy">
+                <param name="s3_key" type="text" label="S3 key to download"
+                       help="Full key of the object to download, e.g. 'sra/SRR000001/SRR000001.sra'.">
+                    <validator type="empty_field" message="An S3 key is required for download."/>
+                    <sanitizer invalid_char="">
+                        <valid initial="string.printable">
+                            <remove value="'"/>
+                            <remove value='"'/>
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
+                       checked="false" label="Download recursively"
+                       help="Download all objects with this prefix rather than a single object."/>
+            </when>
+
+            <!-- ── FASTQ DUMP ── -->
+            <when value="fastq_dump">
+                <param name="accession" type="text" label="SRA Accession"
+                       help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
+                    <validator type="empty_field" message="An SRA accession is required."/>
+                    <validator type="regex"
+                               message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits)."
+                               expression="^[SED]RR[0-9]+$"/>
+                </param>
+                <param name="layout" type="select" label="Read layout"
+                       help="Paired-end produces two datasets labelled accession_1 and accession_2. Single-end produces one dataset. Check the SRA record to confirm layout before running.">
+                    <option value="paired" selected="true">Paired-end (R1 + R2)</option>
+                    <option value="single">Single-end</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <!-- List output -->
+        <data name="output_list" format="txt"
+              label="SRA S3 listing: ${source.prefix}">
+            <filter>action['mode'] == 'list'</filter>
+        </data>
+
+        <!-- Raw download -->
+        <data name="output_data" format="auto"
+              label="SRA download: ${action.s3_key}">
+            <filter>action['mode'] == 'copy'</filter>
+        </data>
+
+        <!-- FASTQ R1 / single.
+             Label matches fasterq-dump's native _1 suffix so Galaxy's
+             "Build List of Dataset Pairs" can auto-detect pairings. -->
+        <data name="output_r1" format="fastqsanger.gz"
+              label="${action.accession}_1">
+            <filter>action['mode'] == 'fastq_dump'</filter>
+        </data>
+
+        <!-- FASTQ R2 (paired-end only) -->
+        <data name="output_r2" format="fastqsanger.gz"
+              label="${action.accession}_2">
+            <filter>action['mode'] == 'fastq_dump' and action['layout'] == 'paired'</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <!-- Test 1: list mode -->
+        <test expect_num_outputs="1">
+            <section name="source">
+                <param name="bucket" value="sra_pub_run_odp"/>
+                <param name="prefix" value="sra/SRR000001"/>
+            </section>
+            <conditional name="action">
+                <param name="mode" value="list"/>
+                <param name="recursive" value="false"/>
+            </conditional>
+            <output name="output_list">
+                <assert_contents>
+                    <has_text text="SRR000001"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test 2: fastq_dump paired -->
+        <test expect_num_outputs="2">
+            <section name="source">
+                <param name="bucket" value="sra_pub_run_odp"/>
+            </section>
+            <conditional name="action">
+                <param name="mode" value="fastq_dump"/>
+                <param name="accession" value="SRR000001"/>
+                <param name="layout" value="paired"/>
+            </conditional>
+            <output name="output_r1">
+                <assert_contents>
+                    <has_text text="@SRR000001"/>
+                </assert_contents>
+            </output>
+            <output name="output_r2">
+                <assert_contents>
+                    <has_text text="@SRR000001"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- Test 3: fastq_dump single-end -->
+        <test expect_num_outputs="1">
+            <section name="source">
+                <param name="bucket" value="sra_pub_run_odp"/>
+            </section>
+            <conditional name="action">
+                <param name="mode" value="fastq_dump"/>
+                <param name="accession" value="SRR000001"/>
+                <param name="layout" value="single"/>
+            </conditional>
+            <output name="output_r1">
+                <assert_contents>
+                    <has_text text="@SRR000001"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**NCBI SRA AWS Fetch**
+
+This tool fetches data from the `NCBI Sequence Read Archive (SRA)`_ hosted on Amazon S3
+as part of the AWS Open Data program. No AWS account is required.
+
+-----
+
+**Available Buckets**
+
++------------------------------+------------------------------------------------------------+
+| Bucket                       | Contents                                                   |
++==============================+============================================================+
+| sra-pub-run-odp              | All open-access SRA runs in SRA Normalized format (.sra).  |
+|                              | Supports FASTQ conversion via this tool.                   |
++------------------------------+------------------------------------------------------------+
+| sra-pub-src-1                | Source BAM, CRAM, and FASTQ files from PacBio, ONT, 10X.  |
++------------------------------+------------------------------------------------------------+
+| sra-pub-src-2                | Same as above (second bucket for source submissions).       |
++------------------------------+------------------------------------------------------------+
+| sra-pub-metadata-us-east-1   | SRA metadata in Parquet/CSV format (for Athena / Glue).    |
++------------------------------+------------------------------------------------------------+
+
+-----
+
+**Listing objects**
+
+Select **List objects** to see what files are available under a given prefix, e.g. ``sra/SRR000001``.
+Leave the prefix blank to browse the bucket root (may return a very large listing).
+
+-----
+
+**Downloading raw files**
+
+Select **Download raw file(s)** and provide the full S3 key, e.g.::
+
+    sra/SRR000001/SRR000001.sra
+
+-----
+
+**Download and convert to FASTQ**
+
+Fetches a single SRA run from ``sra-pub-run-odp`` and converts it to gzip-compressed
+FASTQ using ``fasterq-dump``.
+
+Outputs are labelled ``<accession>_1`` (R1 / forward) and ``<accession>_2`` (R2 / reverse)
+for paired-end runs, matching ``fasterq-dump``'s native ``--split-files`` naming.
+Single-end runs produce only ``<accession>_1``.
+
+*Fetching multiple accessions and building a paired collection*
+
+Run this tool **once per accession** — either manually or by using Galaxy's dataset
+collection mapping to fan out over a list of accession identifiers. Keeping one job per
+accession means a failed download does not affect the others.
+
+Once all jobs are complete your history will contain datasets labelled::
+
+    SRR000001_1    SRR000001_2
+    SRR000002_1    SRR000002_2
+    ...
+
+Use **Galaxy's "Build List of Dataset Pairs"** tool to assemble these into a
+``list:paired`` collection. Galaxy will auto-detect the ``_1`` / ``_2`` suffixes
+and propose pairings — confirm and name the collection, then pass it directly to
+any downstream tool that accepts a paired collection (aligners, QC tools, etc.).
+
+.. warning::
+
+   This tool cannot auto-detect read layout from the accession. Check the SRA record
+   at https://www.ncbi.nlm.nih.gov/sra before running. Selecting the wrong layout will
+   produce incorrect output.
+
+-----
+
+**Notes**
+
+- All S3 requests are made without AWS credentials (``--no-sign-request``).
+- There is typically a **1–2 day lag** between an accession appearing in SRA Search and
+  being available in the S3 buckets.
+- Controlled-access dbGaP data (``sra-ca-run-odp``) requires AWS credentials and is
+  **not** supported by this tool.
+- ``fasterq-dump`` and ``pigz`` both use ``\${GALAXY_SLOTS}`` threads. Allocate more
+  cores in your job configuration to speed up conversion of large runs.
+
+.. _NCBI Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">
+@misc{ncbi_sra_aws,
+  title        = {{NCBI} {SRA} on {AWS} Open Data},
+  author       = {{National Center for Biotechnology Information}},
+  howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
+  note         = {Accessed via AWS S3 without credentials}
+}
+        </citation>
+        <citation type="bibtex">
+@article{sra_toolkit,
+  title   = {The {NCBI} {SRA} and portable data in biology},
+  author  = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
+             {International Nucleotide Sequence Database Collaboration}},
+  journal = {Nucleic Acids Research},
+  volume  = {39},
+  number  = {suppl\_1},
+  pages   = {D19--D21},
+  year    = {2011},
+  doi     = {10.1093/nar/gkq1019}
+}
+        </citation>
+    </citations>
+
+</tool>