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changeset 36:1ec814014652 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
author iuc
date Thu, 14 Mar 2024 15:21:59 +0000
parents de0f7e0a3896
children ba931a59dd59
files fasterq_dump.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/fasterq_dump.xml	Thu Mar 07 07:22:00 2024 +0000
+++ b/fasterq_dump.xml	Thu Mar 14 15:21:59 2024 +0000
@@ -2,6 +2,7 @@
     <description>format from NCBI SRA</description>
     <macros>
         <import>macros.xml</import>
+        <token name="VERSION_SUFFIX">1</token>
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="bio_tools"/>
@@ -13,7 +14,9 @@
     @CONFIGURE_RETRY@
     @SET_ACCESSIONS@
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
-        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
+        fasterq-dump "\$acc"
+        -e \${GALAXY_SLOTS:-1}
+        -t \${TMPDIR}
         --seq-defline '$adv.seq_defline'
         --qual-defline '+'
         $adv.split