diff nucBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,39 @@
+<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>
+        bedtools nuc
+        $strand
+        $seq
+        $pattern
+        $case
+        -fi $fasta 
+        -bed $inputA
+        &gt; $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 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." />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <help>
+
+**What it does**
+
+Profiles the nucleotide content of intervals in a fasta file.
+
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>