From 2d25fd8e5ef005249956691c1782f24e7f95cf03 Mon Sep 17 00:00:00 2001
From: Pavel Dimens <pdimens@live.com>
Date: Mon, 7 Jun 2021 12:26:01 -0400
Subject: [PATCH] add params script

---
 scripts/params | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100755 scripts/params

diff --git a/scripts/params b/scripts/params
new file mode 100755
index 0000000..6cec06c
--- /dev/null
+++ b/scripts/params
@@ -0,0 +1,33 @@
+#! /usr/bin/env bash
+
+if [[ -z "$1" ]]; then
+cat <<EOF
+
+Print the usage information for LepMap3/LepAnchor modules. 
+Should be used in main project directory.
+Module names are case-sensitive.
+
+[usage]:  params <module name>
+[example]:  scripts/params OrderMarkers2 
+
+LepMap3 modules:
+- ParentCall2
+- Filtering2
+- SeparateChromosomes2
+- JoinSingles2All
+- OrderMarkers2 
+
+LepAnchor modules:
+- Map2Bed
+- CleanMap
+- PlaceAndOrientContigs
+
+EOF
+  exit 1
+fi
+
+if [[ $1 == "Map2Bed" || $1 == "CleanMap" || $1 == "PlaceAndOrientContigs" ]]; then
+  java -cp software/LepAnchor $1 2>&1
+else
+  java -cp software/LepMap3 $1 2>&1 |  tail -n +2
+fi
\ No newline at end of file