# HG changeset patch
# User scottx611x
# Date 1532886815 14400
# Node ID c53375e61b33c4473c4da0d475c4c9b2a28550c6
# Parent  e856fda6f375a482eb4d40cd97804b19c2c8bce1
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty

diff -r e856fda6f375 -r c53375e61b33 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Fri Jul 27 11:53:29 2018 -0400
+++ b/qualimap_bamqc.py	Sun Jul 29 13:53:35 2018 -0400
@@ -7,11 +7,10 @@
 import sys
 
 
-def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
+def qualimap_bamqc(bam_filename, out_dir, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
-        "-oc " + genomecov_file,
         "-outdir " + out_dir,
         "--java-mem-size=" + jv_mem_size
     ]
@@ -27,11 +26,9 @@
         description="Generate Bam Quality Statistics"
     )
     parser.add_argument('--input_file')
-    parser.add_argument('--out_genome_file')
     parser.add_argument('--out_dir')
     parser.add_argument('--out_zip')
     parser.add_argument('--out_html')
-    parser.add_argument('--out_results')
     parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
@@ -39,7 +36,6 @@
 
     qualimap_bamqc(
         args.input_file,
-        args.out_genome_file,
         args.out_dir,
         args.java_mem_size
     )
@@ -47,7 +43,7 @@
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        os.path.join(args.out_dir,'raw_data_qualimapReport')
+        os.path.join(args.out_dir, 'raw_data_qualimapReport')
     )
 
     shutil.move("raw_data_qualimapReport.zip", args.out_zip)
@@ -55,10 +51,6 @@
         os.path.join(args.out_dir, "genome_results.txt"),
         args.out_results
     )
-    shutil.move(
-        os.path.join(args.out_dir, "qualimapReport.html"),
-        args.out_html
-    )
 
 if __name__ == "__main__":
     main()
diff -r e856fda6f375 -r c53375e61b33 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Fri Jul 27 11:53:29 2018 -0400
+++ b/qualimap_bamqc.xml	Sun Jul 29 13:53:35 2018 -0400
@@ -12,9 +12,7 @@
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
             --out_dir qualimap_results
-            --out_genome_file $genome_coverage
             --out_zip $raw_data_qualimapReport
-            --out_html $qualimapReport
             --out_results $genome_results
             --java_mem_size $mem_size
     </command>
@@ -23,35 +21,21 @@
         <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="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report for: ${on_string}"></data>
-        <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${on_string}"></data>
-        <data format="html" name="qualimapReport" label="Qualimap BamQC HTML Report for: ${on_string}"></data>
-        <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${on_string}"></data>
+        <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${input_realigned_bam_file}"></data>
+        <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${input_realigned_bam_file}"></data>
     </outputs>
    
     <tests>
         <test>
           <param name="mem_size"  value="2G"></param>
           <param name="input_realigned_bam_file" value="test.bam"></param>
-           <output name="genome_coverage">
-            <assert_contents>
-              <has_text text="#chr  pos coverage" />
-            </assert_contents>
-          </output>
           <output name="genome_results">
           	<assert_contents>
               <has_text text="BamQC report" />
             </assert_contents>
           </output>
-          <output name="qualimapReport">
-          	<assert_contents>
-              <has_text text="Qualimap Report: BAM QC" />
-            </assert_contents>
-          </output>
-          <output name="qualimap_raw_data_results">
-            <assert_contents>
-              <has_text text="" />
-            </assert_contents>
+          <output name="raw_data_qualimapReport" ftype="zip">
+            <metadata name="name" value="raw_data_qualimapReport.zip" />
           </output>
         </test>
     </tests>