changeset 4:a19abfa30ca7 draft

planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159

--- a/qualimap_bamqc.py	Mon Apr 04 04:31:02 2016 -0400
+++ b/qualimap_bamqc.py	Tue Apr 05 03:34:34 2016 -0400
@@ -5,38 +5,40 @@
 import shlex
 import sys
 import logging
-log = logging.getLogger( __name__ )
+
+log = logging.getLogger(__name__)
+
 
-def qualimap_bamqc( bam_filename, genomecov_file, out_dir, pdf_file, jv_mem_size):
-    #qualimap bamqc -bam R.bam.sorted_dedup.bam_realigned.bam -oc ./test.genomecov  -outdir ./Kaust_kxdr/variants/qualimap/bamqc_report --outfile test.pdf --java-mem-size=16G
-    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format( bam_filename,
-                                                                                                     genomecov_file,
-                                                                                                     out_dir,
-                                                                                                     pdf_file,
-                                                                                                     jv_mem_size)
-    cmdline = newSplit(cmdline_str)
+def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
+    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format(bam_filename,
+                                                                                                    genomecov_file,
+                                                                                                    out_dir,
+                                                                                                    jv_mem_size)
+    cmdline = new_split(cmdline_str)
     try:
         check_call(cmdline)
     except CalledProcessError:
         print("Error running the qualimap bamqc", file=sys.stderr)
 
-def newSplit(value):
+
+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_genome_file', default="bam_stats.genomecov")
-    parser.add_argument('--out_dir',  default="/tmp/bamstats")
-    parser.add_argument('--out_pdf_file', default="bam_stats.pdf")
-    parser.add_argument('--java_mem_size', default="8G" )
+    parser.add_argument('--out_dir', default="/tmp/bamstats")
+    parser.add_argument('--java_mem_size', default="8G")
 
     args = parser.parse_args()
-   
-    qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.out_pdf_file, args.java_mem_size)
+
+    qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.java_mem_size)
+
 
 if __name__ == "__main__": main()

--- a/qualimap_bamqc.xml	Mon Apr 04 04:31:02 2016 -0400
+++ b/qualimap_bamqc.xml	Tue Apr 05 03:34:34 2016 -0400
@@ -13,7 +13,6 @@
             --input_file ${input_realigned_bam_file}
             --out_genome_file ${genomecov_file}
             --out_dir ${genomecov_file.files_path}
-            --out_pdf_file ${pdf_file}
             --java_mem_size ${mem_size}
     </command>
     <inputs>
@@ -22,7 +21,6 @@
     </inputs>
     <outputs>
         <data format="genomecov" name="genomecov_file" label="QualiMap: BamQC GenomeCov output"/>
-        <data format="pdf" name="pdf_file" label="QualiMap: BamQC PDF output"/>
     </outputs>
     <help>Help!</help>
     <citations>