diff expandBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/expandBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/expandBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,25 +6,40 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools expand
-        -c $cols
-        -i $inputA
-        &gt; $output
+        -c "${cols}"
+        -i "${input}"
+        > "${output}"
+]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" />
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="choose_columns" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data name="output" metadata_source="input" format_source="input" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="expandBed1.bed" ftype="bed" />
+            <param name="cols" value="5"/>
+            <output name="output" file="expandBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="expandBed1.bed" ftype="bed" />
+            <param name="cols" value="4,5"/>
+            <output name="output" file="expandBed_result2.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>