diff macs2_macros.xml @ 17:35a80f8dda5c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_macros.xml	Sat Feb 15 15:43:39 2014 -0500
@@ -0,0 +1,69 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.0.10.3">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. Per default that option is deactivated: -1.0 (--tsize)" />
+    </xml>
+    <xml name="band_width">
+        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
+            help="This value is only used while building the shifting model. (--bw)" />
+    </xml>
+
+    <token name="@tag_size@">
+        #if $tsize == -1.0:
+            --tsize $tsize
+        #end if
+    </token>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+    </xml>
+
+    <token name="@citation@">
+------
+
+**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 and Bjoern Gruening.
+    </token>
+</macros>