Mercurial > repos > ryotas > cistrome
view peak2gene.xml @ 0:97bd5bb4204c default tip
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author | ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp> |
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date | Tue, 30 Dec 2014 18:45:34 +0900 |
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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>