Mercurial > repos > lparsons > cutadapt
changeset 4:0a872e59164c
Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Wed, 25 May 2011 19:33:40 -0400 |
| parents | 7ed26fc9fa8a |
| children | 1dada50cca8a |
| files | cutadapt.xml discard_stderr_wrapper.sh |
| diffstat | 2 files changed, 42 insertions(+), 2 deletions(-) [+] |
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--- a/cutadapt.xml Wed May 25 18:54:09 2011 -0400 +++ b/cutadapt.xml Wed May 25 19:33:40 2011 -0400 @@ -4,7 +4,7 @@ <requirement type="python-module">cutadapt</requirement> </requirements> - <command>cutadapt + <command interpreter="sh">discard_stderr_wrapper.sh cutadapt #if $input.extension.startswith( "fastq"): --format=fastq #else @@ -30,7 +30,7 @@ #end if '$input' --output='$output' - 2> $report + > $report </command> <inputs> <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/discard_stderr_wrapper.sh Wed May 25 19:33:40 2011 -0400 @@ -0,0 +1,40 @@ +#!/bin/sh + +# STDERR wrapper - discards STDERR if command execution was OK. + +# +# This script executes a given command line, +# while saving the STDERR in a temporary file. +# +# When the command is completed, it checks to see if the exit code was zero. +# if so - the command is assumed to have succeeded - the STDERR file is discarded. +# if not - the command is assumed to have failed, and the STDERR file is dumped to the real STDERR +# +# +# Use this wrapper for tools which insist on writting stuff to STDERR +# even if they succeeded - which throws galaxy off balance. +# +# +# Copyright 2009 (C) by Assaf Gordon +# This file is distributed under the BSD license. +# +# Modified by Lance Parsons (2011) +# Echo STDERR to STDOUT if return code was 0 + +TMPFILE=$(mktemp -t tmp.XXXXXXXXXX) || exit 1 +#CWD=`pwd` +#DIRECTORY=$(cd `dirname $0` && pwd) +#cd $DIRECTORY +"$@" 2> $TMPFILE + +EXITCODE=$? +# Exitcode != 0 ? +if [ "$EXITCODE" -ne "0" ]; then + cat $TMPFILE >&2 +else +# echo "Testing STDOUT" + cat $TMPFILE >&1 +fi +rm $TMPFILE +cd $CWD +exit $EXITCODE