diff macs2_macros.xml @ 1:d202e3d663bb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_macros.xml	Thu Jan 16 15:44:43 2014 -0500
@@ -0,0 +1,49 @@
+<macros>
+    <xml name="requirements">
+        <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>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="conditional_effective_genome_size">
+        <conditional name="effective_genome_size_options">
+            <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
+                <option value="3300000000">Human (3.300.000.000)</option>
+                <option value="3000000000">Mouse (3.000.000.000)</option>
+                <option value="190000000">Fly (190.000.000)</option>
+                <option value="130000000">Worm (130.000.000)</option>
+                <option value="user_defined">User defined</option>
+            </param>
+            <when value="user_defined">
+                <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@effective_genome_size@">
+        #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
+            --gsize $effective_genome_size_options.gsize
+        #else:
+            --gsize $effective_genome_size_options.effective_genome_size_options_selector
+        #end if
+    </token>
+
+    <xml name="version_command">
+        <version_command>macs2 --version</version_command>
+    </xml>
+
+    <xml name="tag_size">
+        <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0)  (--tsize)" />
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Error:" />
+            <regex match="EXception:" />
+        </stdio>
+    </xml>
+</macros>