diff sortBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sortBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,46 @@
+<tool id="bedtools_sortbed" name="Sort BED files" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        sortBed -i $input $option &gt; $output
+    </command>
+    <inputs>
+        <param format="bed" name="input" type="data" label="Sort the following BED file"/>
+        <param name="option" type="select" label="Sort by">
+            <!-- sort -k 1,1 -k2,2 -n a.bed -->
+            <option value="">chromosome, then by start position (asc)</option>
+            <option value="-sizeA">feature size in ascending order.</option>
+            <option value="-sizeD">feature size in descending order.</option>
+            <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
+            <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
+            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
+            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+    </outputs>
+
+    <help>
+
+**What it does**
+
+Sorts a feature file by chromosome and other criteria.
+
+
+.. class:: warningmark
+
+It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
+will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
+by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
+
+@REFERENCES@
+
+    </help>
+    <expand macro="citations" />
+</tool>