diff nucBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/nucBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/nucBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,34 +6,54 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools nuc
         $strand
         $seq
         $pattern
         $case
-        -fi $fasta 
-        -bed $inputA
-        &gt; $output
+        -fi $fasta
+        -bed $input
+        > $output
+]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param format="fasta" name="fasta" type="data" label="Fasta file"/>
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="fasta" name="fasta" type="data" label="FASTA file"/>
 
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." />
-        <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." />
-        <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" label="Report the number of times a user-defined sequence is observed (case-sensitive)." />
-        <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." />
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            label="Profile the sequence according to strand" help="(-s)"/>
+        <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
+            label="Print the extracted sequence" help="(-seq)"/>
+        <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue=""
+            label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" />
+        <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue=""
+            label="Igore case when matching -pattern" help="(-C)"/>
     </inputs>
     <outputs>
-        <data format="fasta" name="output" />
+        <data format="tabular" name="output" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <output name="output" file="nucBed_result1.bed" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="seq" value="True" />
+            <output name="output" file="nucBed_result2.bed" ftype="tabular" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 Profiles the nucleotide content of intervals in a fasta file.
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>