diff macs2_randsample.xml @ 35:2f7d0d0b5bd0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_randsample.xml	Wed Apr 29 12:06:24 2015 -0400
@@ -0,0 +1,54 @@
+<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0">
+    <description>Randomly sample number or percentage of total reads</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 randsample
+            -t "${ infile }"
+            -o "${ outfile }"
+
+        --format '${ infile.extension.upper() }'
+
+        @tag_size@
+        #if $method_options.method_options_selector == 'percentage':
+            --percentage "${ method_options.percentage }"
+        #else:
+            --number "${ method_options.number }"
+        #end if
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <expand macro="tag_size" />
+
+        <conditional name="method_options">
+            <param name="method_options_selector" type="select" label="Select action to be performed">
+                <option value="percentage" selected="true">Percentage</option>
+                <option value="number">Number</option>
+            </param>
+            <when value="percentage">
+                    <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
+            </when>
+            <when value="number">
+                    <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- No test, due to the randomness -->
+    </tests>
+    <help>
+**What it does**
+
+randsample tool from macs2
+
+@citation@
+  </help>
+  <expand macro="citations" />
+</tool>