diff nucBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,59 @@
+<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools nuc
+        $strand
+        $seq
+        $pattern
+        $case
+        -fi $fasta
+        -bed $input
+        > $output
+]]>
+    </command>
+    <inputs>
+        <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" 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="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>