diff vt_normalize.xml @ 0:e4d445a95419 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vt_normalize.xml	Mon Aug 11 14:10:22 2014 -0400
@@ -0,0 +1,55 @@
+<tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
+    <description>normalizes variants in a VCF file</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>vt_macros.xml</import>
+        <token name="@BINARY@">normalize</token>
+    </macros>
+    <command>
+<![CDATA[
+        vt @BINARY@
+            -o "${ outfile }"
+            ##-q  do not print options and summary []
+            -w  window size for local sorting of variants [10000]
+            -I  $intervals_file
+            ##-i  intervals []
+            -r  $reference_genome
+            "${ infile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <param name="reference_genome" type="select" label="Using reference genome">
+              <options from_data_table="fasta_indexes">
+                <filter type="data_meta" ref="infile" key="dbkey" column="1" />
+                <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+              </options>
+        </param>
+
+        <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
+        <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants" 
+            help="(-w)">
+            <validator type="in_range" min="0"/>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases, 
+the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs.
+
+@CITATION@
+    </help>
+    <!--expand macro="citations"/-->
+</tool>