diff slopBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/slopBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,49 @@
+<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools slop
+        $pct
+        $strand
+        -g $genome
+        -i $inputA
+        #if $addition.addition_select == 'b':
+        -b $addition.b
+        #else:
+        -l $addition.l
+        -r $addition.r
+        #end if
+        $header
+
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" 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" />
+        <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the input file prior to results." />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" label=""/>
+    </outputs>
+    <help>
+
+**What it does**
+
+bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
+
+.. image:: $PATH_TO_IMAGES/slop-glyph.png
+
+.. class:: warningmark
+
+In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>