diff macs2_refinepeak.xml @ 0:9c157b556c33 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_refinepeak.xml	Thu Jan 16 13:31:17 2014 -0500
@@ -0,0 +1,46 @@
+<tool id="macs2_refinepeak" name="Refine peak summits" version="2.0.10.0">
+    <description></description>
+    <requirements>
+        <requirement type="python-module">macs2</requirement>
+        <requirement type="python-module">numpy</requirement>
+        <requirement type="package" version="2.0.10.2">macs2</requirement>
+        <requirement type="package" version="1.7.1">numpy</requirement>
+    </requirements>
+    <command>
+
+        macs2 refinepeak
+            -b $bed_infile
+            -i $infile
+            --format '$ifile.extension.upper()'
+            --cutoff $cutoff
+            --window-size $winsize
+            --ofile $ofile
+
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
+        <param name="cutoff" type="float" label="Cutoff" value="5.0" help="DEFAULT: 5.0 (--cutoff)"/>
+        <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="DEFAULT: 200bp (--window-size)" />
+    </inputs>
+
+    <outputs>
+        <data name="ofile" format="bed" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </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**
+
+For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
+
+Integration of MACS2 with Galaxy performed by Ziru Zhou ( [e-mail] ). Please send your comments/questions to modENCODE DCC at [e-mail].
+    </help>
+</tool>