Mercurial > repos > iuc > sra_tools

changeset 23:653e89d73fc4 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 05:06:27 -0400
parents 751a694ec620
children e08a7ad4378b
files fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml
diffstat 4 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fasterq_dump.xml	Mon Jul 20 07:27:41 2020 -0400
+++ b/fasterq_dump.xml	Thu Aug 20 05:06:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" 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 $log;
         if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
             break ;
         else
--- a/fastq_dump.xml	Mon Jul 20 07:27:41 2020 -0400
+++ b/fastq_dump.xml	Thu Aug 20 05:06:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy2" profile="18.01">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
--- a/sam_dump.xml	Mon Jul 20 07:27:41 2020 -0400
+++ b/sam_dump.xml	Thu Aug 20 05:06:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy2" profile="18.01">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
--- a/sra_macros.xml	Mon Jul 20 07:27:41 2020 -0400
+++ b/sra_macros.xml	Thu Aug 20 05:06:27 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.10.7</token>
+    <token name="@VERSION@">2.10.8</token>
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>