diff macs2_bdgdiff.xml @ 0:9c157b556c33 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_bdgdiff.xml	Thu Jan 16 13:31:17 2014 -0500
@@ -0,0 +1,84 @@
+<tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0">
+    <description>based on paired four bedgraph files</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 bdgdiff
+            --t1 $infile_pileup_cond1
+            --t2 $infile_pileup_cond2
+            --c1 $infile_control_cond1
+            --c2 $infile_control_cond2
+            --cutoff $cutoff
+            --min-len $minlen
+            --depth1 $depth1
+            --depth2 $depth2
+
+            # Why does #if '--ofile-cond1' in $outputs not work?
+            #if '--ofile-cond1' in str($outputs).split(','):
+                --ofile-cond1 $output_cond1
+            #end if
+
+            #if '--ofile-cond2' in str($outputs).split(','):
+                --ofile-cond2 $output_cond2
+            #end if
+
+            #if '--ofile-both-conditions' in str($outputs).split(','):
+                --ofile-both-conditions $output_both
+            #end if
+
+    </command>
+    <inputs>
+        <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
+        <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
+
+        <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" />
+        <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" />
+
+        <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="DEFAULT: 1.0 (likelihood ratio=10) (--cutoff)"/>
+        <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/>
+        <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default: 1 (--depth1)" />
+        <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default: 1 (--depth2)" />
+
+        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
+            <option value="--ofile-cond1">Unique regions in condition 1</option>
+            <option value="--ofile-cond2">Unique regions in condition 2</option>
+            <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
+            <validator type="no_options" message="Please select at least one output file." />
+        </param>
+
+    </inputs>
+
+    <outputs>
+        <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (cond 1)">
+            <filter>'--ofile-cond1' in outputs</filter>
+        </data>
+        <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (cond 2)">
+            <filter>'--ofile-cond2' in outputs</filter>
+        </data>
+        <data name="output_both" format="bed" label="${tool.name} on ${on_string} (both)">
+            <filter>'--ofile-both-conditions' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </tests>
+    <help>
+**What it does**
+
+bdgdiff from macs2
+
+
+------
+
+**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>