diff complementBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/complementBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/complementBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,20 +6,29 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         complementBed
-        -d $distance
-        -g genome
-        &gt; $output
+        -i "$input"
+        -g "$genome"
+        > "$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="input" type="data" label="BED/VCF/GFF file"/>
         <expand macro="genome" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Complemen of ${inputA.name}"/>
+        <data format_source="input" name="output" metadata_source="input" label="Complemen of ${input.name}"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="a.bed" ftype="bed" />
+            <param name="genome" value="mm9_chr1.len" />
+            <output name="output" file="complementBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
@@ -27,6 +36,7 @@
 .. image:: $PATH_TO_IMAGES/complement-glyph.png
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>