# HG changeset patch
# User ulfschaefer
# Date 1467987030 14400
# Node ID 9a2a4e1a4a8e003c0afd1dc5abe68efb8e3fd402

Uploaded

diff -r 000000000000 -r 9a2a4e1a4a8e MOST.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MOST.sh	Fri Jul 08 10:10:30 2016 -0400
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+echo $@
+
+FWDFILE=$1
+shift
+REVFILE=$1
+shift
+OUTXML=$1
+shift
+OUTCSV=$1
+shift
+ORGANISM=$1
+
+OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX)
+rm -rf $OUTFOLDER # MOST insists on creating the folder itself
+
+CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM"
+
+echo $CMD
+eval $CMD
+
+STEM=$(basename $FWDFILE)
+STEM="${STEM%.*}"
+
+mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV
+mv "$OUTFOLDER/$STEM.results.xml" $OUTXML
+
+rm -rf $OUTFOLDER