diff --git a/test-data/1.bedgraph b/test-data/1.bedgraph new file mode 100644 index 00000000000..30a4bfcd9f3 --- /dev/null +++ b/test-data/1.bedgraph @@ -0,0 +1,30 @@ +chr1 0 14361 0 +chr1 14361 14829 1 +chr1 14829 14969 0 +chr1 14969 15038 1 +chr1 15038 15795 0 +chr1 15795 15947 1 +chr1 15947 16606 0 +chr1 16606 16765 1 +chr1 16765 16857 0 +chr1 16857 17055 1 +chr1 17055 17232 0 +chr1 17232 17368 1 +chr1 17368 17605 0 +chr1 17605 17742 1 +chr1 17742 17914 0 +chr1 17914 18061 1 +chr1 18061 18267 0 +chr1 18267 18366 1 +chr1 18366 24737 0 +chr1 24737 24891 1 +chr1 24891 29320 0 +chr1 29320 29370 1 +chr1 29370 34610 0 +chr1 34610 35174 2 +chr1 35174 35276 0 +chr1 35276 35481 2 +chr1 35481 35720 0 +chr1 35720 36081 2 +chr1 36081 69090 0 +chr1 69090 69093 3 diff --git a/tools/filters/wig_to_bigwig.xml b/tools/filters/wig_to_bigwig.xml index 6afce203131..e9409f8a25a 100644 --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -1,4 +1,4 @@ - + converter grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 #if $settings.settingsType == "full": @@ -11,7 +11,7 @@ ucsc_tools - + @@ -46,11 +46,16 @@ + + + + + **Syntax** -This tool converts wiggle data into bigWig type. +This tool converts bedgraph or wiggle data into bigWig type. - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. @@ -71,5 +76,9 @@ This tool converts wiggle data into bigWig type. dataValue1 dataValue2 +- The **BedGraph format** is described in detail at the `UCSC Bioinformatics website`_ + +.. _UCSC Bioinformatics website: http://genome.ucsc.edu/goldenPath/help/bedgraph.html +