# HG changeset patch
# User matnguyen
# Date 1542400107 18000
# Node ID 6a73638d707c7c51c7802093523cd670a7186997
Initial Upload
diff -r 000000000000 -r 6a73638d707c tools/concatenator/concatenator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/concatenator/concatenator Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+
+import sys
+import argparse as ap
+
+parser = ap.ArgumentParser(prog='concatenater', conflict_handler='resolve',
+ description="Concatenates all accessions and their associated paths")
+
+input = parser.add_argument_group('Input', '')
+input.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)")
+input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls")
+
+if len(sys.argv) == 1:
+ parser.print_usage()
+ sys.exit(1)
+
+args = parser.parse_args()
+output = open('paths.txt', 'w')
+
+for index,path in enumerate(args.input):
+ output.write("%s=%s\n" % (args.name[index], path))
diff -r 000000000000 -r 6a73638d707c tools/concatenator/concatenator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/concatenator/concatenator.xml Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,27 @@
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+ creates a list of accessions and the associated path to their variant calls
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+ pathogist
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diff -r 000000000000 -r 6a73638d707c tools/consensus_clustering/consensus_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/consensus_clustering/consensus_clustering.xml Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,34 @@
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+ : Performs consensus clustering on multiple clusterings
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+ pathogist
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diff -r 000000000000 -r 6a73638d707c tools/correlation_clustering/correlation_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/correlation_clustering/correlation_clustering.xml Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,31 @@
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+ : Runs correlation clustering on a distance matrix file
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+ pathogist
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diff -r 000000000000 -r 6a73638d707c tools/distance/distance.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/distance/distance.xml Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,32 @@
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+ : Construct distance matrix from genotyping data
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+ pathogist
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diff -r 000000000000 -r 6a73638d707c tools/visualization/visualization.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/visualization/visualization.xml Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,31 @@
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+ : Visualize distance matrix
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+ pathogist
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+ pdf == True
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