Mercurial > repos > iuc > sra_tools

diff fasterq_dump.xml @ 20:b50c21c6e6bb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72"
author iuc
date Thu, 20 Aug 2020 09:05:33 +0000
parents adc510b2288d
children 9828888fc245
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line diff
--- a/fasterq_dump.xml	Mon Jul 06 23:45:55 2020 +0000
+++ b/fasterq_dump.xml	Thu Aug 20 09:05:33 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,6 +6,7 @@
     <expand macro="requirements"/>
     <version_command>fasterq-dump --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+    set -o | grep -q pipefail && set -o pipefail;
     @COPY_CONFIGFILE@
     @SET_ACCESSIONS@
     #if $input.input_select == "file":
@@ -19,7 +20,7 @@
         #if str( $adv.minlen ) != "":
             --min-read-len "$adv.minlen"
         #end if
-        $adv.skip_technical >> $log 2>&1 ;
+        $adv.skip_technical 2>&1 | tee $log;
         if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
             break ;
         else