From d6ce280e7793c78e97612a632c17057ef75f10bb Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Thu, 8 Sep 2016 21:42:07 -0500
Subject: [PATCH] Added 'list' argument to allow vararg inputs. Updated
workflow_module & job accordingly to handle new input type.
---
chipathlon/conf.py | 5 ++++-
chipathlon/workflow_module.py | 9 +++++++++
2 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/chipathlon/conf.py b/chipathlon/conf.py
index 5445f2f..addb191 100644
--- a/chipathlon/conf.py
+++ b/chipathlon/conf.py
@@ -85,9 +85,12 @@ resources = {
# file -> Normal file arguments.
# stdout -> Any file argument that is redirected from stdout
# stderr -> Any file argument that is redirected from stderr
+# list -> For variable argument inputs
+# list -> Currently a list of files.
argument_types = {
"argument": ["string", "numeric"],
- "file": ["file", "rawfile", "stdout", "stderr"]
+ "file": ["file", "rawfile", "stdout", "stderr"],
+ "list": ["list"]
}
# Defines information about arguments
diff --git a/chipathlon/workflow_module.py b/chipathlon/workflow_module.py
index 931b55e..4c958fc 100644
--- a/chipathlon/workflow_module.py
+++ b/chipathlon/workflow_module.py
@@ -396,6 +396,15 @@ class WorkflowModule(object):
"file": master_files[arg_params[param_name]],
"type": param_info["type"]
})
+ elif param_info["type"] in chipathlon.conf.argument_types["list"]:
+ sub_list = []
+ for val in arg_params[param_name]:
+ sub_list.append({
+ "name": val,
+ "file": master_files[val],
+ "type": "file"
+ })
+ param_list.append({"name": arg_params[param_name], "type": "list", "value": sub_list})
else:
param_list.append({
"name": param_name,
--
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