# HG changeset patch
# User dfornika
# Date 1575068093 0
# Node ID d78b129b98c782b2231aa75419f459c70cbee8c0
# Parent  a3f54efeead6092922f1e5f993fce53a85686898
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 92e900f2e63812885018aeaede2e67fbb5fcdddc-dirty"

diff -r a3f54efeead6 -r d78b129b98c7 ncbi_acc_download.xml
--- 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">