Mercurial > repos > dfornika > ncbi_acc_download

changeset 21:d78b129b98c7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 92e900f2e63812885018aeaede2e67fbb5fcdddc-dirty"
author dfornika
date Fri, 29 Nov 2019 22:54:53 +0000
parents a3f54efeead6
children b01c73cb290a
files ncbi_acc_download.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/ncbi_acc_download.xml	Fri Nov 29 22:32:09 2019 +0000
+++ b/ncbi_acc_download.xml	Fri Nov 29 22:54:53 2019 +0000
@@ -14,17 +14,17 @@
         #end if
         mkdir outdir &&
         cd outdir &&
-        while read accession; do
+        for accession in \$(cat accessions); do
         echo "Downloading accession number: " \$accession &&
-        sleep 2 &&
+        sleep 2;
         ncbi-acc-download
             --molecule '${molecule.select}'
             --format '${molecule.format}'
             #if $molecule.format != 'featuretable' and $molecule.format != 'gff3':
                 --extended-validation all
             #end if
-            \${accession};
-        done || exit 1 < ../accessions 2> >(tee -a ../error.log >&2)
+            \${accession}
+        done || exit 1 2> >(tee -a ../error.log >&2)
     ]]></command>
     <inputs>
         <conditional name="query_source">