diff tools/filters/CreateInterval.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/CreateInterval.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,56 @@
+<tool id="createInterval" name="Create single interval">
+  <description>as a new dataset</description>
+  <command interpreter="perl">CreateInterval.pl $chrom $start $end "$name" $strand $out_file1</command>
+  <inputs>
+    <param name="chrom" size="20" type="text" value="chr7" label="Chromosome"/>
+    <param name="start" size="20" type="integer" value="100" label="Start position"/>
+    <param name="end"   size="20" type="integer" value="1000" label="End position"/>
+    <param name="name" size="20" type="text" value="myInterval" label="Name"/>
+    <param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" >
+      <option value="plus">plus</option>
+      <option value="minus">minus</option>
+    </param>    
+  </inputs>
+  <outputs>
+    <data format="bed" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="chrom" value="chr7"/>
+      <param name="start" value="100"/>
+      <param name="end" value="1000"/>
+      <param name="name" value="myinterval"/>
+      <param name="strand" value="plus"/>
+      <output name="out_file1" file="eq-createinterval.dat"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: warningmark
+
+**TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the "?" link in the history item.
+
+-----
+
+**What it does**
+
+This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.
+
+-----
+
+**Example**
+
+Typing the following values in the form::
+
+    Chromosome: chrX
+    Start position: 151087187
+    End position: 151370486
+    Name: NM_000808
+    Strand: minus
+
+will create a single interval::
+
+    chrX  151087187  151370486  NM_000808  0  -
+
+</help>
+</tool>