changeset 0:d00bc4d82e90 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_bamqc.xml	Wed Jul 25 10:54:06 2018 -0400
@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2">
+    <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
+    <requirements>
+        <requirement type="package" version="2.2">qualimap</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="python">
+        qualimap_bamqc.py
+            --input_file $input_realigned_bam_file
+            --out_genome_file $genome_results
+            --out_dir qualimap_results
+            --java_mem_size $mem_size
+    </command>
+    <inputs>
+        <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
+        <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_results" label="Qualimap BamQC report">
+          <discover_datasets pattern="genome_results*" 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*" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
+        </data>
+    </outputs>
+   
+    <tests>
+        <test>
+          <param name="input_realigned_bam_file" value="test.bam"></param>
+          <output name="genome_results">
+            <assert_contents>
+              <has_text text="BamQC report" />
+            </assert_contents>
+          </output>
+          <output name="qualimap_html_results">
+            <assert_contents>
+              <has_text text="Qualimap report: BAM QC" />
+            </assert_contents>
+          </output>
+        </test>
+    </tests>
+    <help>
+        https://github.com/scottx611x/qualimap2
+    </help>
+    <citations>
+    </citations>
+</tool>