diff filter_bed_on_splice_junctions.xml @ 0:915e5c5e02e6 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_bed_on_splice_junctions.xml	Wed Feb 05 08:18:49 2014 -0500
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool id="filter_bed_on_splice_junctions" name="Filter BED on splice junctions" version="0.0.1">
+  <description>that are not in a reference bed file</description>
+  <command interpreter="python">filter_bed_on_splice_junctions.py  --input "$input_bed" 
+  --guided_junctions "$guided_junctions" 
+  #if $leading_bp:
+    --leading_bp $leading_bp
+  #end if
+  #if $trailing_bp:
+    --trailing_bp $trailing_bp
+  #end if
+  --novel_junctions "$novel_junctions"
+  </command>
+  <inputs>
+    <param name="input_bed" type="data" format="bed" label="BED file" 
+           help="e.g. tophat junctions.bed run without GTF option or no-novel-junctions"/> 
+    <param name="guided_junctions" type="data" format="bed" optional="true" label="reference bed file" 
+           help="e.g. tophat junctions.bed run with GTF option and no-novel-junctions"/> 
+    <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Extend the start position" 
+           help="The number of base pairs to extend the start of the exon before the junction position"/>
+    <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Extend the end position" 
+           help="The number of base pairs to extend the end of the exon after the junction position"/>
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data name="novel_junctions" metadata_source="input_bed" format="bed"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_bed" value="novel_splice_junctions.bed" ftype="bed" dbkey="hg19"/>
+      <param name="guided_junctions" value="gtf_splice_junctions.bed" ftype="bed" dbkey="hg19"/>
+      <param name="leading_bp" value="0"/>
+      <param name="trailing_bp" value="0"/>
+      <output name="novel_junctions" file="filtered_novel_splice_junctions.bed"/>
+    </test>
+    <test>
+      <param name="input_bed" value="novel_splice_junctions.bed" ftype="bed" dbkey="hg19"/>
+      <param name="guided_junctions" value="gtf_splice_junctions.bed" ftype="bed" dbkey="hg19"/>
+      <param name="leading_bp" value="10"/>
+      <param name="trailing_bp" value="10"/>
+      <output name="novel_junctions" file="extended_novel_splice_junctions.bed"/>
+    </test>
+  </tests>
+  <help>
+**Filter BED on splice junctions**
+
+Filter out lines of a BED file that have junctions that are in in the reference bed file of known junctions. 
+The start position of the exon preceding the junction and the end position of the exon after the junction can be extended.  
+This is to compensate for alignments that may not include enough of the exons surrounding the junctions.  
+
+A typical application would be to run tophat twice, 
+once with the --GTF and --no-novel-juncs options for well known splice junctions,
+then a second time without those options to also include novel splice junctions.  
+
+This application would filter out the well splice known junctions 
+from the run intended to find all splice junctions including novel ones.
+
+  </help>
+</tool>