1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5fda62776e3d/ changeset: 5fda62776e3d user: jgoecks date: 2013-01-24 23:06:51 summary: Enable BedGraph to be used as input to wig-to-bigwig tool. affected #: 3 files
diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/1.bedgraph --- /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 -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/3.bigwig Binary file test-data/3.bigwig has changed
diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 tools/filters/wig_to_bigwig.xml --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -1,4 +1,4 @@ -<tool id="wig_to_bigWig" name="Wig-to-bigWig" version="1.1.0"> +<tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0"><description>converter</description><command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 #if $settings.settingsType == "full": @@ -11,7 +11,7 @@ <requirement type="package">ucsc_tools</requirement></requirements><inputs> - <param format="wig" name="input1" type="data" label="Convert"> + <param format="wig,bedgraph" name="input1" type="data" label="Convert"><validator type="unspecified_build" /></param><conditional name="settings"> @@ -46,11 +46,16 @@ <param name="settingsType" value="preset" /><output name="out_file1" file="2.bigwig"/></test> + <test> + <param name="input1" value="1.bedgraph" dbkey="hg19" ftype="bedgraph"/> + <param name="settingsType" value="preset" /> + <output name="out_file1" file="3.bigwig"/> + </test></tests><help> **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 @@ 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 + </help></tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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