annotate [APliBio]Nebula tools suite/Nebula/IntersectBed/bedtools_intersectBed.xml @ 1:0ec82f1785af draft

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<tool id="bedtools_intersectBed" name="IntersectBed" version="v2.10.0">
  <description>Report overlaps between two feature files</description>
  <command>bedtools intersect
  
  $invert $count
  
  -f $min_overlap

  #if str($typeA.file_typeA)=="bam"
  -abam $typeA.fileA -b $typeB.fileB > $outbamfile;
  #end if
  
  #if str($typeA.file_typeA)=="bed"
  $report.type_report -a $typeA.fileA -b $typeB.fileB > $outbedfile;
  #end if
  
  #if str($typeA.file_typeA)=="gff"
  $report.type_report -a $typeA.fileA -b $typeB.fileB > $outgfffile;
  #end if
  
  #if str($typeA.file_typeA)=="vcf"
  $report.type_report -a $typeA.fileA -b $typeB.fileB > $outvcffile;
  #end if

  </command>
  <inputs>
    
    <conditional name="typeA">
      <param name="file_typeA" type="select" label="Select the file A type to intersect">
          <option value="bed">BED (.bed)</option>
          <option value="bam">BAM (.bam)</option>
          <option value="vcf">VCF (.vcf)</option>
          <option value="gff">GFF (.gff)</option>
      </param>
    <when value="bam">
      <param name="fileA" format="bam" type="data" label="BAM file"/>
    </when>
    <when value="bed">
     <param name="fileA" format="bed" type="data" label="BED file"/>
    </when>
     <when value="vcf">
      <param name="fileA" format="vcf" type="data" label="VCF file"/>
    </when>
    <when value="gff">
     <param name="fileA" format="gff" type="data" label="GFF file"/>
    </when>
    </conditional>
    
    <conditional name="typeB">
      <param name="file_typeB" type="select" label="Select the file B type to intersect">
          <option value="bed">BED (.bed)</option>
          <option value="vcf">VCF (.vcf)</option>
          <option value="gff">GFF (.gff)</option>
      </param>
    <when value="bed">
     <param name="fileB" format="bed" type="data" label="BED file"/>
    </when>
     <when value="vcf">
      <param name="fileB" format="vcf" type="data" label="VCF file"/>
    </when>
    <when value="gff">
     <param name="fileB" format="gff" type="data" label="GFF file"/>
    </when>
    </conditional>
    
    <conditional name="report">
      <param name="type_report" type="select" label="Select the type of report" help="not used if the file A type is BAM">
         <option value="">write the base-pair overlap between A and B</option>
         <option value="-wa">write the original entry in A for each overlap (-wa)</option>
        <!--  <option value="-wb">-wb : write the original entry in B for each overlap</option> -->
          <option value="-wo">write the original A and B entries plus the number of base pairs of overlap between the two features (-wo)</option>
          <option value="-wao">write the original A and B entries plus the number of base pairs of overlap between the two features (-wao)</option>
      </param>
    <when value="">
     <!-- do nothing here -->
    </when>
    <when value="-wa">
     <!-- do nothing here -->
    </when>
   <!-- <when value="-wb">
    </when> -->
    <when value="-wo">
     <!-- do nothing here -->
    </when>
    <when value="-wao">
    <!-- do nothing here -->
    </when>
    </conditional>
    
  <param name="invert" label="Only report those entries in A that have _no overlaps_ with B?" type="boolean" truevalue="-v" falsevalue="" checked="no"/>
  <param name="count" label="For each entry in A, report the number of overlaps with B?" type="boolean" truevalue="-c" falsevalue=""  checked="no"/>
  
  <param name="min_overlap" type="float" size="10"  value="0.05" label="Minimum overlap required as a fraction of A" help="5% by default" />
  <param name="file_name" type="text" size="20" value="sample" label="File name (without file extension)"/>  
  </inputs>
  
  <outputs>
    <data format="bam" name="outbamfile" label="${file_name}.bam">
      <filter>typeA['file_typeA']=="bam"</filter>
    </data>
   <data format="bed" name="outbedfile" label="${file_name}.bed">
      <filter>typeA['file_typeA']=="bed"</filter>
    </data>
    <data format="gff" name="outgfffile" label="${file_name}.gff">
      <filter>typeA['file_typeA']=="gff"</filter>
    </data>
    <data format="vcf" name="outvcffile" label="${file_name}.vcf">
      <filter>typeA['file_typeA']=="vcf"</filter>
    </data>-->
  </outputs>
  
  <help>
**What it does**

This tool use the "intersectBed" function of Bedtools to report overlaps between two feature files.

Note: When intersecting SNPs, make sure the coordinate conform to the UCSC format.
That is, the start position for each SNP should be SNP position - 1 and the end position should be SNP position. E.g. chr7 10000001 10000002 rs123464

    * Report the base-pair overlap between sequence alignments and genes. 
      $ intersectBed -a reads.bed -b genes.bed 
    * Report whether each alignment overlaps one or more genes. If not, the alignment is not reported. 
      $ intersectBed -a reads.bed -b genes.bed -u 
    * Report those alignments that overlap NO genes. Like "grep -v" 
      $ intersectBed -a reads.bed -b genes.bed -v 
    * Report the number of genes that each alignment overlaps. 
      $ intersectBed -a reads.bed -b genes.bed -c 
    * Report the entire, original alignment entry for each overlap with a gene. 
      $ intersectBed -a reads.bed -b genes.bed -wa 
    * Report the entire, original alignment and genes entries for each overlap plus the number of base pairs. Only reads features with overlap are reported. 
      $ intersectBed -a reads.bed -b genes.bed -wo 
    * Report the entire, original alignment and genes entries for each overlap plus the number of base pairs.  However, alignment features w/o overlap are also reported with a NULL gene feature and overlap = 0.
      $ intersectBed -a reads.bed -b genes.bed -wao 
    * Only report an overlap with a repeat if it spans at least 50% of the exon. 
      $ intersectBed -a exons.bed -b repeatMasker.bed –f 0.50 
    * Only report an overlap if comprises 50% of the structural variant and 50% of the segmental duplication. Thus, it is reciprocally at least a 50% overlap. 
      $ intersectBed -a SV.bed -b segmentalDups.bed –f 0.50 -r 
    * Read BED A from stdin. For example, find genes that overlap LINEs but not SINEs. 
      $ intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v 
    * Retain only single-end BAM alignments that overlap exons. 
      $ intersectBed -abam reads.bam -b exons.bed > reads.touchingExons.bam 
    * Retain only single-end BAM alignments that do not overlap simple sequence repeats. 
      $ intersectBed -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam
      
-----

.. class:: infomark

Contact Bruno Zeitouni ([e-mail]) for any questions or concerns about the Galaxy implementation of IntersectBed.
      
  </help>

</tool>