diff bedpeToBam.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedpeToBam.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,48 @@
+<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools bedpetobam
+            -mapq $mapq
+            -i '$input'
+            -g $genome
+            > '$output'
+]]>
+    </command>
+    <inputs>
+        <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
+        <expand macro="genome" />
+        <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"/>
+    </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.
+
+.. class:: warningmark
+
+BED files must be at least BED4 to create BAM (needs name field).
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>