# HG changeset patch
# User jowong
# Date 1542898064 18000
# Node ID 6c38443b46acc4d2fcba66118cc0b76913db2b07
planemo upload
diff -r 000000000000 -r 6c38443b46ac kwip.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kwip.xml Thu Nov 22 09:47:44 2018 -0500
@@ -0,0 +1,61 @@
+
+ Calculates k-mer weighted inner product, a de novo estimator of genetic similarity
+
+ kwip
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@misc{githubPythonPRINCE,
+ author = {Murray, Kevin},
+ year = {2015},
+ title = {kWIP},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/kdmurray91/kWIPE},
+}
+
+
diff -r 000000000000 -r 6c38443b46ac kwip_postprocess.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kwip_postprocess.py Thu Nov 22 09:47:44 2018 -0500
@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+
+import sys
+import argparse as ap
+import re
+parser = ap.ArgumentParser(prog='kwip_postprocess', conflict_handler='resolve',
+ description="Postprocess galaxy kWIP output")
+
+input = parser.add_argument_group('Input', '')
+input.add_argument('-i', '--input', nargs=1, required=True, help="kWIP galaxy OUTPUT")
+
+
+if len(sys.argv) == 0:
+ parser.print_usage()
+ sys.exit(1)
+
+args = parser.parse_args()
+
+
+with open(args.input[0]) as kwip_output:
+ with open('kwip_postprocess_output.txt', 'w') as output:
+ for line in kwip_output:
+ new_line = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', line)
+ output.write(new_line)
+
+
+
diff -r 000000000000 -r 6c38443b46ac kwip_postprocess.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kwip_postprocess.xml Thu Nov 22 09:47:44 2018 -0500
@@ -0,0 +1,17 @@
+
+ Postprocess kWIP galaxy output
+
+
+
+
+
+
+
+
+This tool processes the kwip galaxy output such that it is in line with the command line
+
+
+
+
diff -r 000000000000 -r 6c38443b46ac tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Nov 22 09:47:44 2018 -0500
@@ -0,0 +1,24 @@
+
+
+
+
+
+
+ https://github.com/kdmurray91/kWIP/releases/download/0.2.0/kwip-binaries_0.2.0.tar.gz
+
+ .
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+