Mercurial > repos > pjbriggs > weeder2

comparison weeder2_wrapper.sh @ 2:3c5f10f7dd40 draft

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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
comparison
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1:571cb77ab9e7 2:3c5f10f7dd40
1 #!/bin/sh -e 1 #!/bin/sh -e
2 # 2 #
3 # Wrapper script to run weeder2 as a Galaxy tool 3 # Wrapper script to run weeder2 as a Galaxy tool
4 # 4 #
5 # Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE MOTIFS_OUT MATRIX_OUT [ ARGS... ] 5 # Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE FREQFILES_DIR MOTIFS_OUT MATRIX_OUT [ ARGS... ]
6 # 6 #
7 # ARGS: one or more arguments to supply directly to weeder2 7 # ARGS: one or more arguments to supply directly to weeder2
8 # 8 #
9 # Process command line 9 # Process command line
10 FASTA_IN=$1 10 FASTA_IN=$1
11 SPECIES_CODE=$2 11 SPECIES_CODE=$2
12 MOTIFS_OUT=$3 12 FREQFILES_DIR=$3
13 MATRIX_OUT=$4 13 MOTIFS_OUT=$4
14 MATRIX_OUT=$5
14 # 15 #
15 # Other arguments 16 # Other arguments
16 ARGS="" 17 ARGS=""
17 while [ ! -z "$5" ] ; do 18 while [ ! -z "$6" ] ; do
18 ARGS="$ARGS $5" 19 ARGS="$ARGS $6"
19 shift 20 shift
20 done 21 done
21 # 22 #
22 # Link to input file 23 # Link to input file
23 ln -s $FASTA_IN 24 ln -s $FASTA_IN
24 # 25 #
26 # Locate the FreqFiles directory
27 if [ $FREQFILES_DIR == "." ] ; then
28 # Use the files in the Weeder2 distribution
29 freqfiles_dir=$WEEDER_FREQFILES_DIR
30 else
31 # Alternative location
32 freqfiles_dir=$FREQFILES_DIR
33 fi
34 #
25 # Link to the FreqFiles directory as weeder2 executable 35 # Link to the FreqFiles directory as weeder2 executable
26 # expects it to be the same directory 36 # expects it to be the same directory
27 freqfiles_dir=$WEEDER_FREQFILES_DIR
28 if [ -d $freqfiles_dir ] ; then 37 if [ -d $freqfiles_dir ] ; then
29 echo "Linking to FreqFiles directory" 38 echo "Linking to FreqFiles directory: $freqfiles_dir"
30 ln -s $freqfiles_dir FreqFiles 39 ln -s $freqfiles_dir FreqFiles
31 else 40 else
32 echo "ERROR FreqFiles directory not found" >&2 41 echo "ERROR FreqFiles directory not found" >&2
33 exit 1 42 exit 1
34 fi 43 fi