diff fisherBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fisherBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -0,0 +1,54 @@
+<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools fisher
+        $strand
+        $split
+        -a $inputA
+        -b $inputB
+        -f $overlap
+        -g $genome
+        $reciprocal
+        $m
+        > $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="genome" />
+        <expand macro="strand2" />
+        <expand macro="split" />
+        <expand macro="overlap" />
+        <expand macro="reciprocal" />
+        <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
+            label="Merge overlapping intervals before looking at overlap" help="(-m)" />
+    </inputs>
+    <outputs>
+        <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="fisherBed1.bed" ftype="bed" />
+            <param name="inputB" value="fisherBed2.bed" ftype="bed" />
+            <param name="genome" value="fisherBed.len" ftype="tabular" />
+            <output name="output" file="fisherBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>