diff randomBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/randomBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,53 @@
+<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools random
+        -g $genome
+        -l $length
+        -n $intervals
+        #if str($seed.seed_choose) == "True":
+            -seed $seed.seed
+        #end if
+        > "$output"
+]]>
+    </command>
+    <inputs>
+        <expand macro="genome" />
+        <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
+        <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
+        <expand macro="seed" />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="genome" value="mm9_chr1.len" />
+            <param name="seed_choose" value="False" />
+            <param name="length" value="5" />
+            <param name="intervals" value="3" />
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="chr1" />
+                    <has_n_columns n="6" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>