diff --git a/README.txt b/README.txt
index 1f55233556a6911e95bd0bd2e6c4c9290751c4ad..3bb0c0598b1f498d87ed0d701361e31e5c6162a5 100644
--- a/README.txt
+++ b/README.txt
@@ -5,11 +5,11 @@ dna_create
 	create an empty container
 
 dna_add
-	dna_add Dname Cname
+	dna_add DName Cname
 	add a document in the container
 
 dna_del
-	dna_del Cname DI
+	dna_del DI Cname
 	delete a document from the container
 
 dna_list
@@ -17,11 +17,11 @@ dna_list
 	display the list of documents in the container
 
 dna_store
-	dna_store [-n_synth int] [-i_error int] [-d_error int] [-s_error int] Cname
+	dna_store [-n_synth int] [-i_error float] [-d_error float] [-s_error float] Cname
 	synthetise the documents of the container into dna molecules
 
 dna_read
-	dna_read Cname DI Dname
+	dna_read [-n_read int] Cname DI Dname
 	sequence a document of the container
 
 dna_workflow
diff --git a/dna_add.sh b/dna_add.sh
index 04d4df8f694e565354cf441447f2955ac3b11498..2dbdb4545b37bb9f6eecf5e3299f4c82c813e4d2 100755
--- a/dna_add.sh
+++ b/dna_add.sh
@@ -9,10 +9,10 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
 
 help_function() {
    echo ""
-   echo "Usage: dna_add container document [-nocd]"
-   echo -e "\tcontainer : path to the container"
-   echo -e "\tdocument : path to the document"
+   echo "Usage: dna_add [-nocd] DName CName"
    echo -e "\t-nocd : turn off channel encoding"
+   echo -e "\tDName : path to the document"
+   echo -e "\tCName : path to the container"
    echo ""
    exit 1 # Exit script after printing help
 }
diff --git a/dna_create.sh b/dna_create.sh
index b1d5c054afebc51a04ec3f131a5e2302f328578d..abf411493aa5baeb52db6a18d7002f1705634399 100755
--- a/dna_create.sh
+++ b/dna_create.sh
@@ -8,11 +8,11 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
 
 help_function() {
    echo ""
-   echo "Usage: dna_create [-sim] [-fl int] [-sp string] container"
+   echo "Usage: dna_create [-sim] [-fl int] [-sp string] CName"
    echo -e "\t-sim : turn on simulator mode"
    echo -e "\t-fl : specify fragment length [default = 100]"
    echo -e "\t-sp : specify spacer [default = AAAAAAAACCCCCCCC]"
-   echo -e "\tcontainer : name of the container"
+   echo -e "\tCName : name of the container"
    echo ""
    exit 1 # Exit script after printing help
 }
diff --git a/dna_del.sh b/dna_del.sh
index 3ae95688c5460d66cc01cb3d2b85774c65aa60ec..003f6a9eb57e39fb88125ec79fd6f61f485b2178 100755
--- a/dna_del.sh
+++ b/dna_del.sh
@@ -8,9 +8,9 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
 
 help_function() {
    echo ""
-   echo "Usage: dna_del container DI"
-   echo -e "\tcontainer : path to the container"
-   echo -e "\tDI : index of the document to delete"
+   echo "Usage: dna_del DI CName"
+   echo -e "\tDI : index of the document to delete in the container"
+   echo -e "\tCName : path to the container"
    echo ""
    exit 1 # Exit script after printing help
 }
@@ -23,10 +23,10 @@ while [[ "$#" -gt 0 ]]; do
 	case "$1" in
 		-h | --help ) help_function ; exit 1 ;;
 		-* ) echo "unknown parameter $1" ; exit 1 ;;
-		* ) if test -z "${container_path:-}" ; then
-				container_path="${1}" ; shift ;
-			elif test -z "${doc_index:-}" ; then
+		* ) if test -z "${doc_index:-}" ; then
 				doc_index="${1}" ; shift ;
+			elif test -z "${container_path:-}" ; then
+				container_path="${1}" ; shift ;
 			else
 				echo "unknown parameter $1" ; exit 1 ;
 			fi ;;
diff --git a/dna_list.sh b/dna_list.sh
index 6dbaba0731839fb60282620420283f0f152cdf53..b008e5c2bde33fa451df26ecc74c3625285196f7 100755
--- a/dna_list.sh
+++ b/dna_list.sh
@@ -12,8 +12,8 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
 
 help_function() {
    echo ""
-   echo "Usage: dna_list container"
-   echo -e "\tcontainer : path to the container"
+   echo "Usage: dna_list CName"
+   echo -e "\tCName : path to the container"
    echo ""
    exit 1 # Exit script after printing help
 }
diff --git a/dna_quick_complete_test.sh b/dna_quick_complete_test.sh
index d43ea1b6fbe3dded6b4cc414942b0f229dde24ea..282c9fe85d9010b789ccb44be4a7b40e66c04830 100755
--- a/dna_quick_complete_test.sh
+++ b/dna_quick_complete_test.sh
@@ -27,7 +27,7 @@ rm -rf "$container_path"
 
 "$commands_dir"/dna_create.sh -sim -fl 100 "$container_path" 
 
-call_function "$commands_dir"/dna_add.sh -nocd "$container_path" "$commands_dir"/documents_test/doc.txt
+call_function "$commands_dir"/dna_add.sh -nocd "$container_path" "$commands_dir"/documents_test/doc_short.txt
 
 #call_function "$commands_dir"/dna_add.sh -nocd "$container_path" "$commands_dir"/documents_test/img_50.png
 
diff --git a/dna_read.sh b/dna_read.sh
index add8ce5a04ba5232694a876bafa92f5f1609682b..5a1f89cf6e2e817fcffd0d3aae3a41de0e3960e6 100755
--- a/dna_read.sh
+++ b/dna_read.sh
@@ -9,11 +9,11 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
 
 help_function () {
    echo ""
-   echo "Usage: dna_read [-n_read int] container DI result"
+   echo "Usage: dna_read [-n_read int] Cname DI Dname"
    echo -e "\t-n_read : number of molecules to read [default = 10*n_frag]"
-   echo -e "\tcontainer : path to the container"
+   echo -e "\tCname : path to the container"
    echo -e "\tDI : index of the document to read"
-   echo -e "\tresult : path to save the document"
+   echo -e "\tDname : path to save the document"
    echo ""
    exit 1 # Exit script after printing help
 }
diff --git a/dna_store.sh b/dna_store.sh
index c9ef3b1b22da3db7ba6e1a55a79032cefc582608..eb05521337ae9969ea7988c1e7586586b1f0cdb4 100755
--- a/dna_store.sh
+++ b/dna_store.sh
@@ -9,12 +9,12 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
 
 help_function() {
    echo ""
-   echo "Usage: dna_store [-n_synth int] [-i_error float] [-d_error float] [-s_error float] container"
+   echo "Usage: dna_store [-n_synth int] [-i_error float] [-d_error float] [-s_error float] CName"
    echo -e "\t-n_synth : specify number of synthesis per fragments [default = 100]"
    echo -e "\t-i_error : specify insertion error rate in synthesis simulation [default = 0]"
    echo -e "\t-d_error : specify deletion error rate in synthesis simulation [default = 0]"
    echo -e "\t-s_error : specify substitution error rate in synthesis simulation [default = 0]"
-   echo -e "\tcontainer : path to the container"
+   echo -e "\tCName : path to the container"
    echo ""
    exit 1 # Exit script after printing help
 }