# HG changeset patch
# User refinery-platform
# Date 1532958970 14400
# Node ID a6d048668f7f169c0cc407d3608ef78311cc5568
planemo upload for repository https://github.com/refinery-platform/qualimap2 commit 88b5467f336ac3b6b5d3a6e824273a183e5184b6
diff -r 000000000000 -r a6d048668f7f qualimap_bamqc.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_bamqc.py Mon Jul 30 09:56:10 2018 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+import os
+from subprocess import check_call, CalledProcessError
+import shutil
+import sys
+
+QUALIMAP_OUPUT_DIR = "qualimap_results"
+
+
+def qualimap_bamqc(bam_filename, jv_mem_size):
+ qualimap_command = [
+ "qualimap", "bamqc",
+ "-bam " + bam_filename,
+ "-outdir " + QUALIMAP_OUPUT_DIR,
+ "--java-mem-size=" + jv_mem_size
+ ]
+
+ try:
+ check_call(qualimap_command)
+ except CalledProcessError:
+ print("Error running the qualimap bamqc", file=sys.stderr)
+
+
+def main():
+ parser = argparse.ArgumentParser(
+ description="Generate Bam Quality Statistics"
+ )
+ parser.add_argument('--input_file')
+ parser.add_argument('--out_dir')
+ parser.add_argument('--out_results')
+ parser.add_argument('--out_zip')
+ parser.add_argument('--java_mem_size')
+
+ args = parser.parse_args()
+
+ qualimap_bamqc(args.input_file, args.java_mem_size)
+
+ shutil.make_archive(
+ 'raw_data_qualimapReport',
+ 'zip',
+ os.path.join(QUALIMAP_OUPUT_DIR, 'raw_data_qualimapReport')
+ )
+
+ shutil.move("raw_data_qualimapReport.zip", args.out_zip)
+ shutil.move(
+ os.path.join(QUALIMAP_OUPUT_DIR, "genome_results.txt"),
+ args.out_results
+ )
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r a6d048668f7f qualimap_bamqc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_bamqc.xml Mon Jul 30 09:56:10 2018 -0400
@@ -0,0 +1,48 @@
+
+
+ Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
+
+ qualimap
+
+
+
+
+
+
+ qualimap_bamqc.py
+ --input_file $input_realigned_bam_file
+ --out_results $genome_results
+ --out_zip $raw_data_qualimapReport
+ --java_mem_size $mem_size
+
+
+
+
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+
+ https://github.com/scottx611x/qualimap2
+
+
+
+
diff -r 000000000000 -r a6d048668f7f test-data/test.bam
Binary file test-data/test.bam has changed
diff -r 000000000000 -r a6d048668f7f tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jul 30 09:56:10 2018 -0400
@@ -0,0 +1,6 @@
+
+
+
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+
+
\ No newline at end of file