diff rm_spurious_events.xml @ 0:119fccb59597 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rm_spurious_events.xml	Thu Oct 22 09:52:51 2015 -0400
@@ -0,0 +1,54 @@
+<tool id="rm_spurious_events.py" name="rm_spurious_events.py" version="1.0">
+  <description>Remove spurious events.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <version_command>python rm_spurious_events.py --version</version_command>
+  <command interpreter="python"><![CDATA[rm_spurious_events.py
+#if $positional_1 and $positional_1 is not None:
+$positional_1
+#end if
+
+#if $threshold and $threshold is not None:
+--threshold $threshold
+#end if
+> $default]]></command>
+  <inputs>
+    <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
+    <param help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/>
+  </inputs>
+  <outputs>
+    <data format="bed" hidden="false" name="default"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="positional_1" value="merged_pcr_dupes_spurious.bed"/>
+      <param name="threshold" value="0.5"/>
+      <output name="default" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Remove spurious events originating from errors in random sequence tags.
+
+This script compares all events sharing the same coordinates. Among each group
+of events the maximum number of PCR duplicates is determined. All events that
+are supported by less than 10 percent of this maximum count are removed.
+
+Input:
+* bed6 file containing crosslinking events with score field set to number of PCR
+  duplicates
+
+Output:
+* bed6 file with spurious crosslinking events removed, sorted by fields chrom,
+  start, stop, strand
+
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: [e-mail]
+Status: Testing
+]]></help>
+  <expand macro="citations" />
+</tool>