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

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<?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>