diff subtractBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subtractBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,64 @@
+<tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools subtract
+        $strand
+        -a $inputA
+        -b $inputB
+        -f $overlap
+        $removeIfOverlap
+        > $output
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="strand2" />
+        <expand macro="overlap" />
+        <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
+            <option value="" selected="True">Dont Remove entire feature on overlap</option>
+            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option>
+            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format_source="inputA" name="output" metadata_source="inputA"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <output name="output" file="subtractBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <param name="overlap" value="0.80" />
+            <output name="output" file="subtractBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <param name="removeIfOverlap" value="-A" />
+            <output name="output" file="subtractBed_result3.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
+
+.. image:: $PATH_TO_IMAGES/subtract-glyph.png
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>