changeset 6:8dff744880cd draft

planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6

--- a/qualimap_bamqc.xml	Tue Apr 05 03:53:28 2016 -0400
+++ b/qualimap_bamqc.xml	Tue Apr 05 04:45:41 2016 -0400
@@ -10,10 +10,10 @@
     </stdio>
     <command interpreter="python">
         qualimap_bamqc.py
-            --input_file ${input_realigned_bam_file}
-            --out_genome_file ${genomecov_file}
-            --out_dir ${genomecov_file.files_path}
-            --java_mem_size ${mem_size}
+            --input_file $input_realigned_bam_file
+            --out_genome_file $genomecov_file
+            --out_dir $genomecov_file.files_path
+            --java_mem_size $mem_size
     </command>
     <inputs>
         <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_multi_bamqc.py	Tue Apr 05 04:45:41 2016 -0400
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+import shlex
+import sys
+import logging
+
+log = logging.getLogger(__name__)
+
+
+def qualimap_multi_bamqc(input_file, out_dir, jv_mem_size):
+    #multi-bamqc -r -d ./bamlistinput.txt -outdir ./Kaust_kxdr/variants/qualimap -outformat PDF --java-mem-size=16G
+    cmdline_str = "qualimap multi-bamqc -r -d {} -outdir {} -outformat PDF --java-mem-size={}".format(input_file,
+                                                                                                      out_dir,
+                                                                                                      jv_mem_size)
+    cmdline = new_split(cmdline_str)
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error running the qualimap multi bamqc", file=sys.stderr)
+
+
+def new_split(value):
+    lex = shlex.shlex(value)
+    lex.quotes = '"'
+    lex.whitespace_split = True
+    lex.commenters = ''
+    return list(lex)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
+    parser.add_argument('--input_file')
+    parser.add_argument('--out_dir', default="/tmp/bamstats")
+    parser.add_argument('--java_mem_size', default="8G")
+
+    args = parser.parse_args()
+
+    qualimap_multi_bamqc(args.input_file, args.out_dir, args.java_mem_size)
+
+
+if __name__ == "__main__": main()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_multi_bamqc.xml	Tue Apr 05 04:45:41 2016 -0400
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<tool id="qualimap_multi_bamqc" name="QualiMap Multi BamQC" version="2.2">
+    <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
+    <requirements>
+        <requirement type="package" version="2.2">qualimap</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="python">
+        qualimap_multi_bamqc.py
+            --input_file $input_realigned_bam_file
+            --out_dir $output1.files_path
+            --java_mem_size $mem_size
+    </command>
+    <inputs>
+        <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
+        <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="output1" label="QualiMap: Multi BamQC PDF output"/>
+    </outputs>
+    <help>Help!</help>
+    <citations>
+        <citation></citation>
+    </citations>
+    <tests>
+        <test>
+        </test>
+    </tests>
+</tool>