Mercurial > repos > dfornika > ncbi_acc_download

changeset 29:94aa25f863d6 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 23:31:08 +0000
parents 3d03487d7529
children e098e839ff97
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 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>