# HG changeset patch
# User dfornika
# Date 1575070268 0
# Node ID 94aa25f863d640c81646a8614e48f90da1af62ad
# Parent  3d03487d7529191d487802b136c03fd72da4f2f1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 92e900f2e63812885018aeaede2e67fbb5fcdddc-dirty"

diff -r 3d03487d7529 -r 94aa25f863d6 ncbi_acc_download.xml
--- a/ncbi_acc_download.xml	Fri Nov 29 23:22:14 2019 +0000
+++ b/ncbi_acc_download.xml	Fri Nov 29 23:31:08 2019 +0000
@@ -14,8 +14,7 @@
         #end if
         mkdir outdir &&
         cd outdir &&
-        for accession in \$(cat ../accessions); do
-        sleep 2 &&
+        while read accession; do
         echo "Downloading accession number: " \$accession &&
         ncbi-acc-download
             --molecule '${molecule.select}'
@@ -23,8 +22,8 @@
             #if $molecule.format != 'featuretable' and $molecule.format != 'gff3':
                 --extended-validation all
             #end if
-            \${accession} 2> >(tee -a ../error.log >&2)
-        done || exit 1
+            \${accession} || echo \$accession >> ../failed.txt && sleep 2;
+        done < ../accessions 2> >(tee -a ../error.log >&2)
     ]]></command>
     <inputs>
         <conditional name="query_source">
@@ -67,6 +66,7 @@
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.ft$" directory="outdir" format="txt"/>
         </collection>
         <data name="error_log" from_work_dir="error.log" label="${tool.name} on ${on_string}: Error Log" format="txt"/>
+        <data name="failed_accessions" from_work_dir="failed.txt" label="${tool.name} on ${on_string}: Failed accessions" format="txt"/>
     </outputs>
     <tests>
         <test>