add params script

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