Mercurial > repos > pjbriggs > weeder2
diff weeder2_wrapper.sh @ 2:3c5f10f7dd40 draft
Updated to tool version 2.0.1 (use data table to locate freqfiles).
author | pjbriggs |
---|---|
date | Fri, 27 Nov 2015 11:06:28 -0500 |
parents | 496bc4eff47e |
children | 89315bdc1a8c |
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--- a/weeder2_wrapper.sh Tue Dec 09 11:27:19 2014 -0500 +++ b/weeder2_wrapper.sh Fri Nov 27 11:06:28 2015 -0500 @@ -2,31 +2,40 @@ # # Wrapper script to run weeder2 as a Galaxy tool # -# Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE MOTIFS_OUT MATRIX_OUT [ ARGS... ] +# Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE FREQFILES_DIR MOTIFS_OUT MATRIX_OUT [ ARGS... ] # # ARGS: one or more arguments to supply directly to weeder2 # # Process command line FASTA_IN=$1 SPECIES_CODE=$2 -MOTIFS_OUT=$3 -MATRIX_OUT=$4 +FREQFILES_DIR=$3 +MOTIFS_OUT=$4 +MATRIX_OUT=$5 # # Other arguments ARGS="" -while [ ! -z "$5" ] ; do - ARGS="$ARGS $5" +while [ ! -z "$6" ] ; do + ARGS="$ARGS $6" shift done # # Link to input file ln -s $FASTA_IN # +# Locate the FreqFiles directory +if [ $FREQFILES_DIR == "." ] ; then + # Use the files in the Weeder2 distribution + freqfiles_dir=$WEEDER_FREQFILES_DIR +else + # Alternative location + freqfiles_dir=$FREQFILES_DIR +fi +# # Link to the FreqFiles directory as weeder2 executable # expects it to be the same directory -freqfiles_dir=$WEEDER_FREQFILES_DIR if [ -d $freqfiles_dir ] ; then - echo "Linking to FreqFiles directory" + echo "Linking to FreqFiles directory: $freqfiles_dir" ln -s $freqfiles_dir FreqFiles else echo "ERROR FreqFiles directory not found" >&2