diff qualimap_bamqc.xml @ 23:cefa83db3ebf draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

--- 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>