view peak2gene.xml @ 0:97bd5bb4204c default tip

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<tool name="peak2gene: Peak Center Annotation" id="ceas_peak2gene">
  <!--<description>Input a peak file, and It will search each peak on UCSC GeneTable to get the refGenes near the peak center.</description>
  -->
  <description>This tool is abolished, please use BETA-minus instead.</description>
  <command interpreter="command">/bin/bash $shscript</command>
  <inputs>
    <param format="bed" name="bfile" type="data" label="BED file(center will be aligned, 100,000 lines max)">
      <validator type="unspecified_build" />
    </param>
    <param name="dist" type="integer" label="Distance from peak center" value="30000">
      <validator type="in_range" max="30000" min="300" message="distance is out of range, distance has to be between 300 to 30000" />
    </param>
    <param name="genetype" type="select" label="which you want to output for gene name">
            <option value="--symbol">Offical gene symbol</option>
            <option value=" ">Refseq gene</option>
    </param>    
    <param name="op" type="select" label="Which gene you want to output. eg) up(uptream of gene overlaps with peak center)">
            <option value="all">all</option>
            <option value="up">up</option>
            <option value="down">down</option>
    </param>
  </inputs>
  <outputs>
    <data format="bed" name="output_gene_annotation" label="annotation for each gene" />
    <data format="bed" name="output_peak_annotation" label="annotation for each peak" />
    <data format="txt" name="log" label="GetRef log" />
  </outputs>
<tests><test>
<param name="bfile" value="peak.bed" />
<param name="dist" value="10000" />
<param name="genome" value="hg19" />
<param name="genetype" value="symbol" />
<param name="op" value="up" />
<param name="outputgenelist" file="PCGA_test_gene_annotation.txt" diff_lines="100"/>
<param name="outputbed" file="PCGA_test_peaks_annotation.txt" diff_ines="100" />
</test></tests>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash

#import os

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

#set $path = $os.path.abspath($__app__.config.tool_path)

lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'`
format=`$path/cistrome/fcfunc.py $bfile`

if [[ ${dollar}lines -gt 500000 ]];then
   echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2
   exit;
fi
if [[ ${dollar}format != "passed" ]]; then
   echo ${dollar}format ${gt}${ad}2
   exit;
fi

#set $advparam = ""
#if $dist
#set $advparam = $advparam+"-d "+str($dist)
#end if

#set $gtpath = os.path.join( os.path.abspath("tool-data"), "ceaslib", "GeneTable", $bfile.metadata.dbkey )

PCGA.py -t $bfile --name=output -g $gtpath --op=$op $genetype $advparam ${ad}${gt} $log
mv output_peaks_annotation.txt $output_peak_annotation
mv output_gene_annotation.txt $output_gene_annotation
    </configfile>
  </configfiles>
  <tests>
    <test>
      <param name="bfile" value="bedfile.bed" ftype="bed"/>
      <param name="dist" value="10000" />
      <param name="genome" value="hg19" />
      <param name="genetype" value="refseq" />
      <param name="op" value="down" />
      <output name="output_gene_annotation" file="getref_result_gene.bed" />
      <output name="output_peak_annotation" file="getref_result_peak.bed" />
    </test>
  </tests>
  <help>
This tool is abolished, please use BETA-minus instead.
  </help>

</tool>