From 38945d0a41b6a4b0d2c6c340963cc23f0d97da03 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 31 May 2024 11:34:06 +0200
Subject: [PATCH] Adds the --template option to obimultiplex

Former-commit-id: 349e9f278abd6a6c258f31d99ea04853a79c62de
---
 cmd/obitools/obimultiplex/main.go    | 11 +++++++++++
 pkg/obitools/obimultiplex/options.go | 23 ++++++++++++++++++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/cmd/obitools/obimultiplex/main.go b/cmd/obitools/obimultiplex/main.go
index 82ed566..bea5bfb 100644
--- a/cmd/obitools/obimultiplex/main.go
+++ b/cmd/obitools/obimultiplex/main.go
@@ -1,6 +1,7 @@
 package main
 
 import (
+	"fmt"
 	"os"
 
 	log "github.com/sirupsen/logrus"
@@ -31,6 +32,16 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
+	if obimultiplex.CLIAskConfigTemplate() {
+		fmt.Print(obimultiplex.CLIConfigTemplate())
+		os.Exit(0)
+	}
+
+	if !obimultiplex.CLIHasNGSFilterFile() {
+		log.Error("You must provide a tag list file following the NGSFilter format")
+		os.Exit(1)
+	}
+
 	sequences, err := obiconvert.CLIReadBioSequences(args...)
 
 	if err != nil {
diff --git a/pkg/obitools/obimultiplex/options.go b/pkg/obitools/obimultiplex/options.go
index 28723f1..8f590fa 100644
--- a/pkg/obitools/obimultiplex/options.go
+++ b/pkg/obitools/obimultiplex/options.go
@@ -13,6 +13,7 @@ import (
 )
 
 var _NGSFilterFile = ""
+var _askTemplate = false
 var _UnidentifiedFile = ""
 var _AllowedMismatch = int(2)
 var _AllowsIndel = false
@@ -30,7 +31,6 @@ var _ConservedError = false
 func MultiplexOptionSet(options *getoptions.GetOpt) {
 	options.StringVar(&_NGSFilterFile, "tag-list", _NGSFilterFile,
 		options.Alias("t"),
-		options.Required("You must provide a tag list file following the NGSFilter format"),
 		options.Description("File name of the NGSFilter file describing PCRs."))
 
 	options.BoolVar(&_ConservedError, "keep-errors", _ConservedError,
@@ -47,6 +47,10 @@ func MultiplexOptionSet(options *getoptions.GetOpt) {
 		options.Alias("e"),
 		options.Description("Used to specify the number of errors allowed for matching primers."))
 
+	options.BoolVar(&_askTemplate, "template", _askTemplate,
+		options.Description("Print on the standard output an example of CSV configuration file."),
+	)
+
 }
 
 func OptionSet(options *getoptions.GetOpt) {
@@ -69,6 +73,10 @@ func CLIConservedErrors() bool {
 	return _UnidentifiedFile != "" || _ConservedError
 }
 
+func CLIHasNGSFilterFile() bool {
+	return _NGSFilterFile != ""
+}
+
 func CLINGSFIlter() (obingslibrary.NGSLibrary, error) {
 	file, err := os.Open(_NGSFilterFile)
 
@@ -85,3 +93,16 @@ func CLINGSFIlter() (obingslibrary.NGSLibrary, error) {
 
 	return ngsfiler, nil
 }
+
+func CLIAskConfigTemplate() bool {
+	return _askTemplate
+}
+
+func CLIConfigTemplate() string {
+	return `experiment,sample,sample_tag,forward_primer,reverse_primer
+wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,15a_F730814,gaagtag:gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,26a_F040644,gaatatc:-,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+wolf_diet,29a_F260619,-:-,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
+`
+}