# HG changeset patch
# User scottx611x
# Date 1532635133 14400
# Node ID cefa83db3ebf0754b8a603e6d179603e2caae34e
# Parent  ffc7fdae906ced3c0e7ecc40669a1d8d5fe305e9
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r ffc7fdae906c -r cefa83db3ebf qualimap_bamqc.py
--- a/qualimap_bamqc.py	Thu Jul 26 15:36:54 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 15:58:53 2018 -0400
@@ -2,18 +2,16 @@
 from __future__ import print_function
 import argparse
 from subprocess import check_call, CalledProcessError
+import shutil
 import sys
-import logging
-
-log = logging.getLogger(__name__)
 
 
-def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
+def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
         "-oc " + genomecov_file,
-        "-outdir " + out_dir,
+        "-outdir .",
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -28,19 +26,24 @@
         description="Generate Bam Quality Statistics"
     )
     parser.add_argument('--input_file')
-    parser.add_argument('--out_genome_file', default="genome_coverage.txt")
-    parser.add_argument('--out_dir', default="qualimap_results")
-    parser.add_argument('--java_mem_size', default="8G")
+    parser.add_argument('--out_genome_file')
+    parser.add_argument('--java_mem_size')
 
     args = parser.parse_args()
 
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
-        args.out_dir,
         args.java_mem_size
     )
 
+    shutil.make_archive(
+        'raw_data_qualimapReport.zip',
+        'zip',
+        'qualimap_results/raw_data_qualimapReport/'
+    )
+
+
 
 if __name__ == "__main__":
     main()
diff -r ffc7fdae906c -r cefa83db3ebf qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 15:36:54 2018 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 26 15:58:53 2018 -0400
@@ -11,7 +11,6 @@
     <command interpreter="python">
         qualimap_bamqc.py
             --input_file $input_realigned_bam_file
-            --out_dir qualimap_results
             --out_genome_file $genome_coverage
             --java_mem_size $mem_size
     </command>
@@ -20,16 +19,10 @@
         <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"></data>
-        <data format="txt" name="genome_results" label="Qualimap BamQC Results">
-          <discover_datasets pattern="genome_results.txt" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
-        </data>
-        <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML Report">
-          <discover_datasets pattern="qualimapReport.html" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
-        </data>
-        <data format="txt" name="qualimap_raw_data_results" label="Qualimap Raw Data Results">
-          <discover_datasets pattern="__designation_and_ext__" visible="true" ext="txt" directory="qualimap_results/raw_data_qualimapReport"/>
-        </data>
+        <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="qualimap_html_results" 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>
     </outputs>
    
     <tests>