diff windowBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/windowBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,75 @@
+<tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools window
+        #if $inputA.ext == "bam":
+            -abam $inputA
+        #else:
+            -a $inputA
+        #end if
+        -b $inputB
+        $ubam
+        $bed
+        $strandB
+        #if $addition.addition_select == 'b':
+        -w $addition.b
+        #elif $addition.addition_select == 'lr':
+        -l $addition.l
+        -r $addition.r
+        #end if
+        $original
+        $number
+        $nooverlaps
+        $header
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
+        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param name="ubam" type="boolean" checked="false" truevalue="-ubam" falsevalue="" label="Write uncompressed BAM output" />
+        <param name="bed" type="boolean" checked="false" truevalue="bed" falsevalue="" label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file" />
+        <conditional name="addition">
+            <param name="addition_select" type="select" label="Choose what you want to do">
+                <option value="huhn" selected="True">Do not change added base pairs</option>
+                <option value="b">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
+                <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
+            </param>
+            <when value="b">
+                <param name="b" label="Give Value" type="integer" value="1000"  />
+            </when>
+            <when value="lr">
+                <param name="l" label="Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000"  />
+                <param name="r" label="Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000"  />
+            </when>
+        </conditional>
+        <param name="strandB" type="select" label="Calculation based on strandedness?">
+            <option value="" selected="True">Report any hit in B</option>
+            <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
+            <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
+        </param>
+        <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue="" label="Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B" />
+        <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" label="For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B" />
+        <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Only report those entries in A that have no overlaps with B" />
+        <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results" />
+
+    </inputs>
+    <outputs>
+        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+    </outputs>
+    <help>
+
+**What it does**
+
+Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
+
+.. image:: $PATH_TO_IMAGES/window-glyph.png
+
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>