diff macs2_refinepeak.xml @ 0:fe62ba547975 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_refinepeak.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,45 @@
+<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
+    <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 refinepeak
+            -b "${ bed_infile }"
+            -i "${ infile }"
+            --format '${ infile.extension.upper() }'
+            --cutoff "${ cutoff }"
+            --window-size "${ winsize }"
+            --ofile "${ outfile }"
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
+        <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
+        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="ChIP_200K.bed" ftype="bed"/>
+            <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/>
+            <param name="cutoff" value="5.0"/>
+            <param name="winsize" value="200"/>
+            <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>