# HG changeset patch
# User scottx611x
# Date 1532705306 14400
# Node ID 407b6a65c867af05f90b583d805db1d43377a58c
# Parent  0e6aeed62025ab5f3e9940b9b04233b331cf89e6
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

diff -r 0e6aeed62025 -r 407b6a65c867 qualimap_bamqc.py
--- a/qualimap_bamqc.py	Thu Jul 26 16:57:57 2018 -0400
+++ b/qualimap_bamqc.py	Fri Jul 27 11:28:26 2018 -0400
@@ -6,8 +6,6 @@
 import shutil
 import sys
 
-OUTPUT_DIR = "qualimap_results"
-
 
 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
     qualimap_command = [
@@ -35,6 +33,8 @@
 
     args = parser.parse_args()
 
+    output_dir = os.path.dirname(args.out_genome_file)
+
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
@@ -42,19 +42,24 @@
         args.java_mem_size
     )
 
-    print(os.listdir(os.getcwd()))
-    print(os.listdir(args.out_dir))
+    print(os.listdir(output_dir))
 
-    shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt")
-    shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html")
     shutil.make_archive(
-        './raw_data_qualimapReport',
+        'raw_data_qualimapReport',
         'zip',
         args.out_dir + '/raw_data_qualimapReport'
     )
 
-    print(os.listdir(os.getcwd()))
-    print(os.listdir(args.out_dir))
+    [
+        shutil.move(os.path.join(output_dir, file_name), file_name)
+        for file_name in [
+            "genome_results.txt",
+            "qualimapReport.html",
+            "raw_data_qualimapReport.zip"
+        ]
+    ]
+
+    print(os.listdir(output_dir))
 
 if __name__ == "__main__":
     main()
diff -r 0e6aeed62025 -r 407b6a65c867 qualimap_bamqc.xml
--- a/qualimap_bamqc.xml	Thu Jul 26 16:57:57 2018 -0400
+++ b/qualimap_bamqc.xml	Fri Jul 27 11:28:26 2018 -0400
@@ -22,7 +22,7 @@
     <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="qualimap_html_results" label="Qualimap BamQC HTML Report 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>
     </outputs>
    
@@ -40,7 +40,7 @@
               <has_text text="BamQC report" />
             </assert_contents>
           </output>
-          <output name="qualimap_html_results">
+          <output name="qualimapReport">
           	<assert_contents>
               <has_text text="Qualimap Report: BAM QC" />
             </assert_contents>