diff mergeBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergeBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,147 @@
+<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
+    <description>(mergeBed)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        mergeBed
+            -i "${input}"
+            $strand
+            -d $distance
+            $header
+            @C_AND_O_ARGUMENT@
+            > "${output}"
+]]>
+    </command>
+    <inputs>
+        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
+        <param name="strand" type="select" label="Calculation based on strandedness?">
+            <option value="" selected="True">Overlaps on either strand</option>
+            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
+            <option value="-S +">Force merge for forward strand only.</option>
+            <option value="-S -">Force merge for reverse strand only.</option>
+        </param>
+        <param name="distance" type="integer" value="0"
+            label="Maximum distance between features allowed for features to be merged"
+            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
+        <expand macro="print_header" />
+        <expand macro="c_and_o_argument" />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="mergedBed1.bed" ftype="bed" />
+            <output name="output" file="mergedBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="mergedBed2.bed" ftype="bed" />
+            <param name="strandedness" value="-s" />
+            <output name="output" file="mergedBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="mergedBed3.bed" ftype="bed" />
+            <param name="report_number" value="-n" />
+            <output name="output" file="mergedBed_result3.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="mergedBed4.bed" ftype="bed" />
+            <param name="distance" value="1000" />
+            <output name="output" file="mergedBed_result4.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="mergedBed4.bed" ftype="bed" />
+            <param name="distance" value="1000" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="1"/>
+                <param name="operation" value="count"/>
+            </repeat>
+            <output name="output" file="mergedBed_result5.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
+
+
+.. image:: $PATH_TO_IMAGES/merge-glyph.png
+
+
+.. class:: warningmark
+
+bedtools merge requires that you presort your data by chromosome and then by start position.
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
+bookended intervals into a single, "flattened" or "merged" interval.
+
+::
+
+  $ cat A.bed
+  chr1  100  200
+  chr1  180  250
+  chr1  250  500
+  chr1  501  1000
+
+  $ bedtools merge -i A.bed
+  chr1  100  500
+  chr1  501  1000
+
+
+==========================================================================
+*-s* Enforcing "strandedness"
+==========================================================================
+The ``-s`` option will only merge intervals that are overlapping/bookended
+*and* are on the same strand.
+
+::
+
+  $ cat A.bed
+  chr1  100  200   a1  1 +
+  chr1  180  250   a2  2 +
+  chr1  250  500   a3  3 -
+  chr1  501  1000  a4  4 +
+
+  $ bedtools merge -i A.bed -s
+  chr1  100  250    +
+  chr1  501  1000   +
+  chr1  250  500    -
+
+
+==========================================================================
+*-d* Controlling how close two features must be in order to merge 
+==========================================================================
+By default, only overlapping or book-ended features are combined into a new 
+feature. However, one can force ``merge`` to combine more distant features 
+with the ``-d`` option. For example, were one to set ``-d`` to 1000, any 
+features that overlap or are within 1000 base pairs of one another will be 
+combined.
+
+::
+
+  $ cat A.bed
+  chr1  100  200
+  chr1  501  1000
+  
+  $ bedtools merge -i A.bed
+  chr1  100  200
+  chr1  501  1000
+
+  $ bedtools merge -i A.bed -d 1000
+  chr1  100  200  1000
+
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>