From 1193591b568cebd23a1dfe8823366e0f3e527bcc Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 27 Sep 2019 13:15:53 +0200
Subject: [PATCH] Add parser for dppp csv step into cwl
---
...parse_dppp_parameters_tsv_to_step_input.py | 22 +++++++++++++++++++
1 file changed, 22 insertions(+)
create mode 100644 utils/parse_dppp_parameters_tsv_to_step_input.py
diff --git a/utils/parse_dppp_parameters_tsv_to_step_input.py b/utils/parse_dppp_parameters_tsv_to_step_input.py
new file mode 100644
index 00000000..9540a839
--- /dev/null
+++ b/utils/parse_dppp_parameters_tsv_to_step_input.py
@@ -0,0 +1,22 @@
+#/usr/bin/env python3
+import sys
+
+
+def print_step(line):
+ line_parsed = list(map(lambda x: x.strip(), line))
+ if len(line_parsed) < 4:
+ return
+ parameter_name, type_name, default, doc = line_parsed
+ parameter_name = parameter_name.strip('.').replace('<step>.', '')
+ print('- id: %s\n type: %s\n default: %s\n doc: %s\n'
+ ' inputBinding:\n prefix: %s=\n separate: false' % (parameter_name,
+ type_name,
+ default,
+ doc,
+ parameter_name))
+
+
+lines = [line.split('\t') for line in open(sys.argv[1]).read().splitlines()]
+for line in lines:
+ if line:
+ print_step(line)
--
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