diff tools/qualimap_parser/qualimap_parser.xml @ 0:45533fb9d2f4 draft default tip

Primary version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/qualimap_parser/qualimap_parser.xml	Tue Sep 04 02:49:49 2018 -0400
@@ -0,0 +1,31 @@
+<tool id="parse_qualimap" name="Parse Qualimap reports" version="0.1.0">
+    <description>and output a list of outliers</description>
+    <command><![CDATA[
+        $__tool_directory__/qualimap_parser -n #for $report in $reports# ${report.element_identifier} #end for#
+        -i #for $report in $reports# $report #end for#
+    ]]></command>
+    <inputs>
+        <param name="reports" type="data" format="txt" label="Qualimap Genome Report" help="" optional="false" multiple="True" />
+    </inputs>
+    <outputs>
+        <data name="output_file" label="Outliers from dataset after mapping" format="txt" from_work_dir="outlier_list.txt"/>
+    </outputs>
+
+    <tests>
+        <test>
+
+        </test>
+    </tests>
+
+    <help><![CDATA[
+    Parses Qualimap reports and outputs a list of outliers based on percentage of the reference genome covered and mean mapping quality.
+
+    Command line:
+    qualimap_parser -n <accessions> -i <reports>
+
+    ]]></help>
+
+    <citations>
+        Manuscript in preparation
+    </citations>
+</tool>