diff complementBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/complementBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,42 @@
+<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        complementBed
+        -i "$input"
+        -g "$genome"
+        > "$output"
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="genome" />
+    </inputs>
+    <outputs>
+        <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.
+
+.. image:: $PATH_TO_IMAGES/complement-glyph.png
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>