diff flankBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flankBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -0,0 +1,72 @@
+<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        flankBed
+        $pct
+        $strand
+        -g $genome
+        -i $input
+
+        #if $addition.addition_select == 'b':
+            -b $addition.b
+        #else:
+            -l $addition.l
+            -r $addition.r
+        #end if
+        > $output
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="genome" />
+        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
+            label="Define -l and -r as a fraction of the feature’s length"
+            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            label="Define -l and -r based on strand"
+            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
+        <expand macro="addition" />
+    </inputs>
+    <outputs>
+        <data metadata_source="input" format_source="input" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="a.bed" ftype="bed" />
+            <param name="genome" value="mm9_chr1.len"/>
+            <param name="addition_select" value="b"/>
+            <param name="b" value="5"/>
+            <output name="output" file="flankBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="a.bed" ftype="bed" />
+            <param name="genome" value="mm9_chr1.len"/>
+            <param name="addition_select" value="lr"/>
+            <param name="l" value="2"/>
+            <param name="r" value="3"/>
+            <output name="output" file="flankBed_result2.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
+
+.. image:: $PATH_TO_IMAGES/flank-glyph.png
+
+.. class:: warningmark
+
+In order to prevent creating intervals that violate chromosome boundaries, bedtools flank requires a genome file defining the length of each chromosome or contig.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>