diff macs2_randsample.xml @ 0:9c157b556c33 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_randsample.xml	Thu Jan 16 13:31:17 2014 -0500
@@ -0,0 +1,62 @@
+<tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0">
+    <description>of total reads</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 randsample
+            -t $infile
+            -o $outfile
+
+        --format '$ifile.extension.upper()'
+
+        --tsize $tsize
+        #if str($method_options.method_options_selector ) == 'percentage':
+            $method_options.percentage
+        #else:
+            $method_options.number
+        #end if
+
+    </command>
+    <inputs>
+
+        <!--may need to add a few more formats at later time-->
+        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0)  (--tsize)" />
+
+        <conditional name="method_options">
+            <param name="method_options_selector" type="select" label="Select action to be performed">
+                <option value="percentage">Percentage</option>
+                <option value="number">Number</option>
+            </param>
+            <when value="percentage">
+                    <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
+            </when>
+            <when value="number">
+                    <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
+  </outputs>
+  <tests>
+    <!--none yet for macs2-->
+  </tests>
+  <help>
+**What it does**
+
+randsample tool 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>