From eba5f0f5fd3395cb95adf9306149b917ac755d1a Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Thu, 28 Apr 2022 14:25:36 +0200
Subject: [PATCH] updated readme and params
---
README.txt | 8 ++++----
dna_add.sh | 6 +++---
dna_create.sh | 4 ++--
dna_del.sh | 12 ++++++------
dna_list.sh | 4 ++--
dna_quick_complete_test.sh | 2 +-
dna_read.sh | 6 +++---
dna_store.sh | 4 ++--
8 files changed, 23 insertions(+), 23 deletions(-)
diff --git a/README.txt b/README.txt
index 1f55233..3bb0c05 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 04d4df8..2dbdb45 100755
--- a/dna_add.sh
+++ b/dna_add.sh
@@ -9,10 +9,10 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
help_function() {
echo ""
- echo "Usage: dna_add container document [-nocd]"
- echo -e "\tcontainer : path to the container"
- echo -e "\tdocument : path to the document"
+ echo "Usage: dna_add [-nocd] DName CName"
echo -e "\t-nocd : turn off channel encoding"
+ echo -e "\tDName : path to the document"
+ echo -e "\tCName : path to the container"
echo ""
exit 1 # Exit script after printing help
}
diff --git a/dna_create.sh b/dna_create.sh
index b1d5c05..abf4114 100755
--- a/dna_create.sh
+++ b/dna_create.sh
@@ -8,11 +8,11 @@ source "$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 3ae9568..003f6a9 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 $1" ; exit 1 ;
fi ;;
diff --git a/dna_list.sh b/dna_list.sh
index 6dbaba0..b008e5c 100755
--- a/dna_list.sh
+++ b/dna_list.sh
@@ -12,8 +12,8 @@ source "$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 d43ea1b..282c9fe 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 add8ce5..5a1f89c 100755
--- a/dna_read.sh
+++ b/dna_read.sh
@@ -9,11 +9,11 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
help_function () {
echo ""
- echo "Usage: dna_read [-n_read int] container DI result"
+ echo "Usage: dna_read [-n_read int] Cname DI Dname"
echo -e "\t-n_read : number of molecules to read [default = 10*n_frag]"
- echo -e "\tcontainer : path to the container"
+ echo -e "\tCname : path to the container"
echo -e "\tDI : index of the document to read"
- echo -e "\tresult : path to save the document"
+ echo -e "\tDname : path to save the document"
echo ""
exit 1 # Exit script after printing help
}
diff --git a/dna_store.sh b/dna_store.sh
index c9ef3b1..eb05521 100755
--- a/dna_store.sh
+++ b/dna_store.sh
@@ -9,12 +9,12 @@ source "$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
}
--
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