diff bedpeToBam.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/bedpeToBam.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/bedpeToBam.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,24 +6,33 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools bedpetobam
-        $ubam
-        -mapq $mapq
-        -i '$input'
-        -g $genome
-        &gt; '$output'
+            -mapq $mapq
+            -i '$input'
+            -g $genome
+            > '$output'
+]]>
     </command>
     <inputs>
-        <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
         <expand macro="genome" />
-        <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
-        <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
+        <param name="mapq" type="integer" value="255"
+            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
+            help="(-mapq)" />
     </inputs>
     <outputs>
-        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
+        <data format="bam" name="output" metadata_source="input"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
+            <param name="genome" value="mm9.len"/>
+            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 Converts feature records to BAM format.
@@ -33,6 +42,7 @@
 BED files must be at least BED4 to create BAM (needs name field).
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>