diff jaccardBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/jaccardBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/jaccardBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,29 +6,44 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools jaccard
-        
-        $reciprocal
-        $strand
-        $split
-        -f $overlap 
-        -a $inputA
-        -b $inputB
-        &gt; $output
+            $strand
+            $split
+            $reciprocal
+            -f $overlap
+            -a $inputA
+            -b $inputB
+            > $output
+]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
         <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
-        <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" />
-
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B" />
-        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" label="Report extract sequences in a tab-delimited format instead of in FASTA format." />
-    <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand" />
+        <expand macro="overlap" />
+        <expand macro="reciprocal" />
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 
+            label="Force strandedness"
+            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" />
         <expand macro="strand2" />
+        <expand macro="split" />
     </inputs>
     <outputs>
         <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
+            <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
+            <param name="overlap" value="0.1" />
+            <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
 
 **What it does**