diff slopBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/slopBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/slopBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,34 +6,56 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools slop
         $pct
         $strand
         -g $genome
         -i $inputA
         #if $addition.addition_select == 'b':
-        -b $addition.b
+            -b $addition.b
         #else:
-        -l $addition.l
-        -r $addition.r
+            -l $addition.l
+            -r $addition.r
         #end if
         $header
-
-        &gt; $output
+        > $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" />
+        <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="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." />
+        <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" label=""/>
+        <data format="bed" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="a.bed" ftype="bed" />
+            <param name="genome" value="mm9_chr1.len" ftype="bed" />
+            <param name="addition_select" value="b" />
+            <param name="b" value="5" />
+            <output name="output" file="slopBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="a.bed" ftype="bed" />
+            <param name="genome" value="mm9_chr1.len" ftype="bed" />
+            <param name="addition_select" value="lr" />
+            <param name="l" value="2" />
+            <param name="r" value="3" />
+            <output name="output" file="slopBed_result2.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **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).
@@ -44,6 +66,7 @@
 
 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>