# HG changeset patch # User rlegendre # Date 1406618057 14400 # Node ID d7006c780d35ab87f15476f8f8fc4395ae7299da Uploaded diff -r 000000000000 -r d7006c780d35 ving_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ving_wrapper.xml Tue Jul 29 03:14:17 2014 -0400 @@ -0,0 +1,152 @@ + + + R + Bioconductor + GenomicRanges + Rsamtools + + Visualization of NGS data + + + ./ving.R + #for $i in $series + #set $index = os.popen("samtools index " + str($i.bamfile) + " " + str($i.bamfile) + ".bai") + ${i.bamfile} --description-data=${i.description} + #end for + --output=$output + #if $normalizationCoefficient + --normalization-coefficient=$normalizationCoefficient + #end if + #if str($strand) == 'yes': + --inverseStrand + #end if + --chromosome-name=$chrom + --start=$start + --end=$end + #if $annotation.gff == 'yes': + #for $f in $annotation.serie + --annotation=${f.ownFile} + #end for + --typeTranscript=${annotation.typeTranscript} + --annotation-colors=${annotation.annotColor} + --annotation-shapes=${annotation.shapes} + ${annotation.annotationColorByStrand} + #end if + #if $visuType.visu == 'classic': + --typeVisu=classic + --classic-plus-color=${visuType.plusColor} + --classic-minus-color=${visuType.minusColor} + #elif $visuType.visu == 'heatmap': + --typeVisu=heatmap + --heatmap-max-color=${visuType.heatmapMax} + --heatmap-min-color=${visuType.heatmapMin} + --heatmap-palette-method=${visuType.method} + #else: + --typeVisu=lines + --lines-samples-colors=${visuType.linesColors} + --lines-samples-type-line=${visuType.linesType} + #end if + $scaleLog + $symetricScale + $unstrand + $annotationPlacedByStrand + #if $smoothLength + --smoothLength=$smoothLength + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Summary +------- + +This program uses the `Ving`_ R library. + +.. _Ving: http://vm-gb.curie.fr/ving/ + + + +Dependances +------------ + +.. class:: warningmark + +This tool depends on R (>=3.0.2) and samtools. + + + + +