| Previous changeset 18:18aeac3cd1db (2017-10-21) Next changeset 20:df56e1b12d0c (2018-01-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8 |
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modified:
bedToBam.xml bedpeToBam.xml complementBed.xml coverageBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml multiIntersectBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml test-data/reldistBed_result1.bed test-data/shuffleBed_result1.bed test-data/shuffleBed_result2.bed test-data/shuffleBed_result3.bed test-data/shuffleBed_result4.bed test-data/spacingBed_result1.bed unionBedGraphs.xml |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 bedToBam.xml --- a/bedToBam.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/bedToBam.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0"> <description>converter</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 bedpeToBam.xml --- a/bedpeToBam.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/bedpeToBam.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0"> <description>converter</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 complementBed.xml --- a/complementBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/complementBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0"> <description>Extract intervals not represented by an interval file</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 coverageBed.xml --- a/coverageBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/coverageBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> <description>of features in file B on the features in file A (bedtools coverage)</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 fisherBed.xml --- a/fisherBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/fisherBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0"> <description>calculate Fisher statistic between two feature files</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 flankBed.xml --- a/flankBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/flankBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0"> <description>create new intervals from the flanks of existing intervals</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 genomeCoverageBed.xml --- a/genomeCoverageBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/genomeCoverageBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> <description>compute the coverage over an entire genome</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 macros.xml --- a/macros.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/macros.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,11 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.26.0gx">bedtools</requirement> + <requirement type="package" version="2.27.0">bedtools</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.26.0</token> + <token name="@WRAPPER_VERSION@">2.27.0</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 makeWindowsBed.xml --- a/makeWindowsBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/makeWindowsBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0"> <description>make interval windows across a genome</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 mapBed.xml --- a/mapBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/mapBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0"> <description>apply a function to a column for each overlapping interval</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 maskFastaBed.xml --- a/maskFastaBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/maskFastaBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -9,10 +9,11 @@ <![CDATA[ bedtools maskfasta $soft - -mc "${mc}" - -fi "${fasta}" - -bed "${input}" - -fo "${output}" + -mc '${mc}' + -fi '${fasta}' + -bed '${input}' + -fo '${output}' + $fullheader ]]> </command> <inputs> @@ -24,6 +25,9 @@ <param name="mc" type="text" value="N" label="Replace masking character" help="That is, instead of masking with Ns, use another character. (-mc)" /> + <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue="" + label="Use full fasta header." + help="By default, only the word before the first space or tab is used"/> </inputs> <outputs> <data format="fasta" name="output" /> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 multiIntersectBed.xml --- a/multiIntersectBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/multiIntersectBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0"> <description>identifies common intervals among multiple interval files</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 randomBed.xml --- a/randomBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/randomBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0"> <description>generate random intervals in a genome</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 reldist.xml --- a/reldist.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/reldist.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -25,8 +25,8 @@ </outputs> <tests> <test> - <param name="inputA" value="windowBed_result1.bed" ftype="bed" /> - <param name="inputB" value="windowBed_result1.bed" ftype="bed" /> + <param name="inputA" value="a.bed" ftype="bed" /> + <param name="inputB" value="a.bed" ftype="bed" /> <output name="output" file="reldistBed_result1.bed" ftype="bed" /> </test> </tests> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 shuffleBed.xml --- a/shuffleBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/shuffleBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> <description>randomly redistrubute intervals in a genome</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 slopBed.xml --- a/slopBed.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/slopBed.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0"> <description>adjust the size of intervals</description> <macros> <import>macros.xml</import> |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/reldistBed_result1.bed --- a/test-data/reldistBed_result1.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/reldistBed_result1.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,2 +1,2 @@ reldist count total fraction -0.00 1 1 1.000 +0.00 4 4 1.000 |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/shuffleBed_result1.bed --- a/test-data/shuffleBed_result1.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/shuffleBed_result1.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,2 +1,2 @@ -chr2 5070 5170 a1 1 + -chr1 2199 3199 a2 2 - +chr2 51 151 a1 1 + +chr2 720 1720 a2 2 - |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/shuffleBed_result2.bed --- a/test-data/shuffleBed_result2.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/shuffleBed_result2.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,2 +1,2 @@ -chr1 9383 9483 a1 1 + -chr1 886 1886 a2 2 - +chr1 5845 5945 a1 1 + +chr1 6139 7139 a2 2 - |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/shuffleBed_result3.bed --- a/test-data/shuffleBed_result3.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/shuffleBed_result3.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,2 +1,2 @@ -chr2 5070 5170 a1 1 + -chr1 2199 3199 a2 2 - +chr2 51 151 a1 1 + +chr2 720 1720 a2 2 - |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/shuffleBed_result4.bed --- a/test-data/shuffleBed_result4.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/shuffleBed_result4.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,2 +1,2 @@ -chr2 5070 5170 a1 1 + -chr3 4411 5000 a2 2 - +chr2 51 151 a1 1 + +chr2 720 1720 a2 2 - |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 test-data/spacingBed_result1.bed --- a/test-data/spacingBed_result1.bed Sat Oct 21 07:57:53 2017 -0400 +++ b/test-data/spacingBed_result1.bed Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ chr1 100 200 . -chr1 180 250 0 +chr1 180 250 -1 chr1 250 500 0 chr1 501 1000 1 |
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| diff -r 18aeac3cd1db -r a8eabd2838f6 unionBedGraphs.xml --- a/unionBedGraphs.xml Sat Oct 21 07:57:53 2017 -0400 +++ b/unionBedGraphs.xml Fri Dec 08 03:26:42 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> <description>combines coverage intervals from multiple BEDGRAPH files</description> <macros> <import>macros.xml</import> |