# HG changeset patch # User jbrayet # Date 1451999152 18000 # Node ID 0d3b8e48c42368b726d6b540fc6c5eecd57caa99 # Parent 9947321ac2a041f8da29b544b867a3446d9a2bbe Uploaded diff -r 9947321ac2a0 -r 0d3b8e48c423 annotateGenes_hist_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotateGenes_hist_wrapper.xml Tue Jan 05 08:05:52 2016 -0500 @@ -0,0 +1,146 @@ + + + Caclulates statistics for TSS and gene body + + institutcuriengsintegration/annotategeneshistones:1.0 + + +#if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotateGenes_hist_wrapper.sh -f $inputfile -y $log -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotateGenes_hist_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPNG -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotateGenes_hist_wrapper.sh -y $log -f $inputfile -e $regfile -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotateGenes_hist_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotateGenes_hist_wrapper.sh -f $inputfile -y $log -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotateGenes_hist_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPDF -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotateGenes_hist_wrapper.sh -y $log -f $inputfile -e $regfile -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotateGenes_hist_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 1 #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (if_PDF == 0) + + + (if_PDF == True) + + + + + + (use_control['use_control_selector'] == 'yes') + + + +**What it does** + +This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution + + +