From 2fb11ccc64c88f52dd431eb1f94906d6c0d7a9f0 Mon Sep 17 00:00:00 2001
From: Thomas Jakob Zajac <zajac.thomas1992@gmail.com>
Date: Wed, 21 Dec 2016 15:31:00 +0100
Subject: [PATCH] Enhancement

Former runModelPolisher.sh is now called ModelPolisherTemplate.sh and
contains all options.
---
 scripts/ModelPolisherTemplate.sh | 34 ++++++++++++++++++++++++++++++++
 scripts/runModelPolisher.sh      |  3 ++-
 2 files changed, 36 insertions(+), 1 deletion(-)
 create mode 100644 scripts/ModelPolisherTemplate.sh

diff --git a/scripts/ModelPolisherTemplate.sh b/scripts/ModelPolisherTemplate.sh
new file mode 100644
index 00000000..8643d5ab
--- /dev/null
+++ b/scripts/ModelPolisherTemplate.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+#
+# Launches the ModelPolisher with the options given below.
+#
+# Author: Andreas Draeger, University of California, San Diego.
+#
+## Find location of this script ##
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+${DIR}/ModelPolisher.sh \
+--user=[USER NAME] \
+[
+OPTIONAL:
+--host=[HOST NAME] \
+--port=[PORT] \
+]
+--dbname=[DATABASE NAME] \
+--passwd=[DB USER'S PASSWORD] \
+--input=[INPUT FILE or DIRECTORY] \
+--output=[OUTPUT FILE or DIRECTORY] \
+--compression-type=GZIP \
+--check-mass-balance=true \
+--sbml-validation=true \
+--omit-generic-terms=false \
+--log-level=INFO \
+--log-file=${DIR}/model_polisher.log 2>/dev/null \
+--annotate-with-bigg=false [USE BIGG DB FOR ANNOTATION?] \
+--include-any-uri=false \
+--flux-coefficients=[COMMA SEPARATED LIST] \
+--flux-objectives=[COLON SEPARATED LIST] \
+--document-title-pattern="[biggId] - [organism]" \
+--document-notes-file="SBMLDocumentNotes.html" \
+--model-notes-file="ModelNotes.html"
+exit 0
diff --git a/scripts/runModelPolisher.sh b/scripts/runModelPolisher.sh
index 03a8cd93..77af1a6c 100755
--- a/scripts/runModelPolisher.sh
+++ b/scripts/runModelPolisher.sh
@@ -85,7 +85,7 @@ then
 fi
 if [ -n "$FLUX_OBJECTIVES" ]
 then
-    ARGS+=" --flux-objectives=FLUX_OBJECTIVES$"
+    ARGS+=" --flux-objectives=$FLUX_OBJECTIVES"
 fi
 if [ -n "$DOCUMENT_TITLE_PATTERN" ]
 then
@@ -102,3 +102,4 @@ fi
 
 ${DIR}/ModelPolisher.sh $ARGS
 exit 0
+