Mercurial > repos > galaxytrakr > aws_sra

changeset 10:4bd2a27d3755 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit be05af327782763c7179b8b67ab5ee6a956c81a3
author galaxytrakr
date Mon, 23 Mar 2026 19:09:24 +0000
parents 40b61da6c6c5
children 696191ca014e
files aws_sra.xml
diffstat 1 files changed, 7 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/aws_sra.xml	Mon Mar 23 18:55:11 2026 +0000
+++ b/aws_sra.xml	Mon Mar 23 19:09:24 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.9" profile="23.0">
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.10" profile="23.0">
     <description>Fetch SRA data files from NCBI's public AWS S3 buckets</description>
 
     <requirements>
@@ -27,12 +27,12 @@
             #if $source.prefix
                 #set $s3_path = $s3_path + '/' + $source.prefix.strip("/")
             #end if
-            aws s3 ls \
-                --no-sign-request \
+            aws s3 ls
+                --no-sign-request
                 #if $action.recursive
                     --recursive
-                #end if \
-                $s3_path/ \
+                #end if
+                $s3_path/
             > '$output_list'
 
         ## ── DOWNLOAD RAW mode ────────────────────────────────────────────────────
@@ -49,30 +49,18 @@
         #elif $action.mode == 'fastq_dump'
             #set $acc = $action.accession.strip()
 
-            ## 1. Download the file from S3 (CORRECTED: single line command)
             mkdir -p sra_cache &&
             aws s3 cp --no-sign-request '${s3_base}/sra/${acc}/${acc}' ./sra_cache/${acc} &&
-
-            ## 2. Convert with fasterq-dump
             mkdir -p fastq_out &&
-            fasterq-dump \
-                ./sra_cache/${acc} \
-                --outdir ./fastq_out \
-                --temp . \
-                --threads \${GALAXY_SLOTS:-4} \
-                --split-files
-            &&
-
-            ## 3. Compress with pigz
+            fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
             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>