| Previous changeset 10:c78cf6fe3018 (2016-10-03) Next changeset 12:7b3aaff0d78c (2016-10-28) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 |
|
modified:
annotateBed.xml closestBed.xml clusterBed.xml coverageBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml jaccardBed.xml macros.xml makeWindowsBed.xml mapBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml shuffleBed.xml slopBed.xml sortBed.xml spacingBed.xml subtractBed.xml test-data/annotateBed_result.bed test-data/makeWindowBed_result3.bed test-data/makeWindowBed_result4.bed unionBedGraphs.xml windowBed.xml |
|
removed:
tool_dependencies.xml |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 annotateBed.xml --- a/annotateBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/annotateBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0"> <description>annotate coverage of features from multiple files</description> <macros> <import>macros.xml</import> @@ -52,10 +52,10 @@ </conditional> <expand macro="strand2" /> <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" - label="Report the count of features followed by the % coverage for each annotation file" + label="Report the count of features followed by the % coverage for each annotation file" help="Default is to report solely the fraction of -i covered by each file." /> <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" - label="Report the count of features followed by the % coverage for each annotation file" + label="Report the count of features followed by the % coverage for each annotation file" help="Default is to report solely the fraction of the input file covered by each file." /> </inputs> <outputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 closestBed.xml --- a/closestBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/closestBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -25,7 +25,7 @@ #end if -a '$inputA' -b '$inputBs' - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 clusterBed.xml --- a/clusterBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/clusterBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -10,16 +10,16 @@ bedtools cluster $strand -d $distance - -i $inputA - > $output + -i '$inputA' + > '$output' ]]> </command> <inputs> <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> - <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." + <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." help="That is, only cluster features that are the same strand. By default, this is disabled." /> - <param name="distance" type="integer" value="0" - label="Maximum distance between features allowed for features to be clustered" + <param name="distance" type="integer" value="0" + label="Maximum distance between features allowed for features to be clustered" help="Default is 0. That is, overlapping and/or book-ended features are clustered." /> </inputs> <outputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 coverageBed.xml --- a/coverageBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/coverageBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -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> @@ -24,7 +24,7 @@ <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" /> <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" /> <expand macro="split" /> - <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" + <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/> <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each A feature" @@ -47,10 +47,10 @@ <![CDATA[ **What it does** -`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in -file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments -(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. -One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that +`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in +file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments +(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. +One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A. |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 fisherBed.xml --- a/fisherBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/fisherBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -10,13 +10,13 @@ bedtools fisher $strand $split - -a $inputA - -b $inputB + -a '$inputA' + -b '$inputB' -f $overlap -g $genome $reciprocal $m - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 flankBed.xml --- a/flankBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/flankBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -11,7 +11,7 @@ $pct $strand -g $genome - -i $input + -i '$input' #if $addition.addition_select == 'b': -b $addition.b @@ -19,7 +19,7 @@ -l $addition.l -r $addition.r #end if - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 genomeCoverageBed.xml --- a/genomeCoverageBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/genomeCoverageBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -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> @@ -158,7 +158,7 @@ * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2. **Example Output**: - + chr2L 0 1379895 23011544 0.0599653 chr2L 1 837250 23011544 0.0363839 chr2L 2 904442 23011544 0.0393038 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 getfastaBed.xml --- a/getfastaBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/getfastaBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -24,7 +24,6 @@ </command> <inputs> <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> - <conditional name="fasta_source"> <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file"> <option value="history" selected="True">History</option> @@ -36,7 +35,7 @@ <when value="preloaded"> <param name="fasta_id" type="select"> <options from_data_table="all_fasta" /> - </param> + </param> </when> </conditional> <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 groupbyBed.xml --- a/groupbyBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/groupbyBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -8,17 +8,17 @@ <command> <![CDATA[ bedtools groupby + -i "${inputA}" + -g '$group' -c "${cols}" - -g $group -o $operation - -i "${inputA}" > "${output}" ]]> </command> <inputs> <param format="bed" name="inputA" type="data" label="BED file"/> <expand macro="choose_columns" /> - <param name="group" type="text" value="1,2,3" + <param name="group" type="text" value="1,2,3" label="Specifies which column(s) (1-based) should be used to group the input" help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)"> <sanitizer invalid_char=""> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 jaccardBed.xml --- a/jaccardBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/jaccardBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -12,9 +12,9 @@ $split $reciprocal -f $overlap - -a $inputA - -b $inputB - > $output + -a '$inputA' + -b '$inputB' + > '$output' ]]> </command> <inputs> @@ -22,7 +22,7 @@ <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> <expand macro="overlap" /> <expand macro="reciprocal" /> - <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" + <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" /> <expand macro="strand2" /> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 macros.xml --- a/macros.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/macros.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,11 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.24">bedtools</requirement> + <requirement type="package" version="2.26.0gx">bedtools</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.24</token> + <token name="@WRAPPER_VERSION@">2.26.0</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> @@ -55,19 +55,19 @@ </xml> <xml name="closest_D_option"> <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - label="Ignore features in B that are upstream of features in A" + label="Ignore features in B that are upstream of features in A" help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" - label="Ignore features in B that are downstream of features in A" + label="Ignore features in B that are downstream of features in A" help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue="" - label="Choose first from features in B that are upstream of features in A" + label="Choose first from features in B that are upstream of features in A" help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-fu)" /> <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue="" - label="Choose first from features in B that are downstream of features in A" + label="Choose first from features in B that are downstream of features in A" help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" /> </xml> <xml name="addition"> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 makeWindowsBed.xml --- a/makeWindowsBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/makeWindowsBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -9,9 +9,9 @@ <![CDATA[ bedtools makewindows #if $type.type_select == 'genome': - -g $type.genome + -g '$type.genome' #else: - -b $type.input + -b '$type.input' #end if #if $action.action_select == 'windowsize': -w $action.windowsize @@ -23,7 +23,7 @@ -s $action.step_size #end if $sourcename - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 mapBed.xml --- a/mapBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/mapBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -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> @@ -26,7 +26,7 @@ <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" /> <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" /> <expand macro="overlap" /> - <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" + <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Require reciprocal overlap" help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" /> <expand macro="strand2" /> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 mergeBed.xml --- a/mergeBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/mergeBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.0"> <description>combine overlapping/nearby intervals into a single interval</description> <macros> <import>macros.xml</import> @@ -120,12 +120,12 @@ ========================================================================== -*-d* Controlling how close two features must be in order to merge +*-d* Controlling how close two features must be in order to merge ========================================================================== -By default, only overlapping or book-ended features are combined into a new -feature. However, one can force ``merge`` to combine more distant features -with the ``-d`` option. For example, were one to set ``-d`` to 1000, any -features that overlap or are within 1000 base pairs of one another will be +By default, only overlapping or book-ended features are combined into a new +feature. However, one can force ``merge`` to combine more distant features +with the ``-d`` option. For example, were one to set ``-d`` to 1000, any +features that overlap or are within 1000 base pairs of one another will be combined. :: @@ -133,7 +133,7 @@ $ cat A.bed chr1 100 200 chr1 501 1000 - + $ bedtools merge -i A.bed chr1 100 200 chr1 501 1000 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 multiCov.xml --- a/multiCov.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/multiCov.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -13,10 +13,10 @@ #end for bedtools multicov - -bed $input + -bed '$input' -bams #for $i, $bam in enumerate( $bams ): - ${i}.bam + '${i}.bam' #end for $strand -f $overlap @@ -26,7 +26,7 @@ $duplicate $failed $proper - > $output + > '$output' ]]> </command> <inputs> @@ -43,7 +43,7 @@ label="Include duplicate reads" help="Default counts non-duplicates only. (-D)" /> <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" - label="Include failed-QC reads" + label="Include failed-QC reads" help="Default counts pass-QC reads only (-F)"/> <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Only count proper pairs" |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 multiIntersectBed.xml --- a/multiIntersectBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/multiIntersectBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -50,7 +50,7 @@ </when> </conditional> <expand macro="genome" /> - <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" + <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" label="Invoke Ryan Layers's clustering algorithm" help="(-cluster)" /> <param name="zero" type="boolean" checked="true" @@ -119,11 +119,11 @@ chr1 10 20 chr1 22 27 chr1 24 30 - + # b.bed chr1 12 32 chr1 14 30 - + # c.bed chr1 8 15 chr1 10 14 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 nucBed.xml --- a/nucBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/nucBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -12,9 +12,9 @@ $seq $pattern $case - -fi $fasta - -bed $input - > $output + -fi '$fasta' + -bed '$input' + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 overlapBed.xml --- a/overlapBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/overlapBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -8,9 +8,9 @@ <command> <![CDATA[ bedtools overlap - -i $input + -i '$input' -cols $cols - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 shuffleBed.xml --- a/shuffleBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/shuffleBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -8,8 +8,8 @@ <command> <![CDATA[ bedtools shuffle - -g $genome - -i $inputA + -g '$genome' + -i '$inputA' $bedpe #if str($seed.seed_choose) == "True": -seed $seed.seed @@ -25,7 +25,7 @@ $no_overlap $allow_beyond -maxTries $maxtries - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 slopBed.xml --- a/slopBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/slopBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -10,8 +10,8 @@ bedtools slop $pct $strand - -g $genome - -i $inputA + -g '$genome' + -i '$inputA' #if $addition.addition_select == 'b': -b $addition.b #else: @@ -19,7 +19,7 @@ -r $addition.r #end if $header - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 sortBed.xml --- a/sortBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/sortBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -7,14 +7,14 @@ <expand macro="stdio" /> <command> <![CDATA[ - sortBed - -i $input - $option - > $output + sortBed + -i '$input' + $option + > '$output' ]]> </command> <inputs> - <param format="bed" name="input" type="data" label="Sort the following BED file"/> + <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/> <param name="option" type="select" label="Sort by"> <!-- sort -k 1,1 -k2,2 -n a.bed --> <option value="">chromosome, then by start position (asc)</option> @@ -27,7 +27,7 @@ </param> </inputs> <outputs> - <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> + <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/> </outputs> <tests> <test> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 spacingBed.xml --- a/spacingBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/spacingBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -8,8 +8,8 @@ <command> <![CDATA[ bedtools spacing - -i $input - > $output + -i '$input' + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 subtractBed.xml --- a/subtractBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/subtractBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -9,11 +9,11 @@ <![CDATA[ bedtools subtract $strand - -a $inputA - -b $inputB + -a '$inputA' + -b '$inputB' -f $overlap $removeIfOverlap - > $output + > '$output' ]]> </command> <inputs> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 test-data/annotateBed_result.bed --- a/test-data/annotateBed_result.bed Mon Oct 03 07:36:08 2016 -0400 +++ b/test-data/annotateBed_result.bed Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,4 +1,4 @@ -# annotateBed2.bed annotateBed3.bed annotateBed4.bed +# annotateBed2.bed annotateBed3.bed annotateBed4.bed chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000 chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000 chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 test-data/makeWindowBed_result3.bed --- a/test-data/makeWindowBed_result3.bed Mon Oct 03 07:36:08 2016 -0400 +++ b/test-data/makeWindowBed_result3.bed Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,100 +1,100 @@ -chr1 0 1971955 -chr1 1971955 3943910 -chr1 3943910 5915865 -chr1 5915865 7887820 -chr1 7887820 9859775 -chr1 9859775 11831730 -chr1 11831730 13803685 -chr1 13803685 15775640 -chr1 15775640 17747595 -chr1 17747595 19719550 -chr1 19719550 21691505 -chr1 21691505 23663460 -chr1 23663460 25635415 -chr1 25635415 27607370 -chr1 27607370 29579325 -chr1 29579325 31551280 -chr1 31551280 33523235 -chr1 33523235 35495190 -chr1 35495190 37467145 -chr1 37467145 39439100 -chr1 39439100 41411055 -chr1 41411055 43383010 -chr1 43383010 45354965 -chr1 45354965 47326920 -chr1 47326920 49298875 -chr1 49298875 51270830 -chr1 51270830 53242785 -chr1 53242785 55214740 -chr1 55214740 57186695 -chr1 57186695 59158650 -chr1 59158650 61130605 -chr1 61130605 63102560 -chr1 63102560 65074515 -chr1 65074515 67046470 -chr1 67046470 69018425 -chr1 69018425 70990380 -chr1 70990380 72962335 -chr1 72962335 74934290 -chr1 74934290 76906245 -chr1 76906245 78878200 -chr1 78878200 80850155 -chr1 80850155 82822110 -chr1 82822110 84794065 -chr1 84794065 86766020 -chr1 86766020 88737975 -chr1 88737975 90709930 -chr1 90709930 92681885 -chr1 92681885 94653840 -chr1 94653840 96625795 -chr1 96625795 98597750 -chr1 98597750 100569705 -chr1 100569705 102541660 -chr1 102541660 104513615 -chr1 104513615 106485570 -chr1 106485570 108457525 -chr1 108457525 110429480 -chr1 110429480 112401435 -chr1 112401435 114373390 -chr1 114373390 116345345 -chr1 116345345 118317300 -chr1 118317300 120289255 -chr1 120289255 122261210 -chr1 122261210 124233165 -chr1 124233165 126205120 -chr1 126205120 128177075 -chr1 128177075 130149030 -chr1 130149030 132120985 -chr1 132120985 134092940 -chr1 134092940 136064895 -chr1 136064895 138036850 -chr1 138036850 140008805 -chr1 140008805 141980760 -chr1 141980760 143952715 -chr1 143952715 145924670 -chr1 145924670 147896625 -chr1 147896625 149868580 -chr1 149868580 151840535 -chr1 151840535 153812490 -chr1 153812490 155784445 -chr1 155784445 157756400 -chr1 157756400 159728355 -chr1 159728355 161700310 -chr1 161700310 163672265 -chr1 163672265 165644220 -chr1 165644220 167616175 -chr1 167616175 169588130 -chr1 169588130 171560085 -chr1 171560085 173532040 -chr1 173532040 175503995 -chr1 175503995 177475950 -chr1 177475950 179447905 -chr1 179447905 181419860 -chr1 181419860 183391815 -chr1 183391815 185363770 -chr1 185363770 187335725 -chr1 187335725 189307680 -chr1 189307680 191279635 -chr1 191279635 193251590 -chr1 193251590 195223545 -chr1 195223545 197195432 +chr1 0 1971954 +chr1 1971954 3943908 +chr1 3943908 5915862 +chr1 5915862 7887816 +chr1 7887816 9859770 +chr1 9859770 11831724 +chr1 11831724 13803678 +chr1 13803678 15775632 +chr1 15775632 17747586 +chr1 17747586 19719540 +chr1 19719540 21691494 +chr1 21691494 23663448 +chr1 23663448 25635402 +chr1 25635402 27607356 +chr1 27607356 29579310 +chr1 29579310 31551264 +chr1 31551264 33523218 +chr1 33523218 35495172 +chr1 35495172 37467126 +chr1 37467126 39439080 +chr1 39439080 41411034 +chr1 41411034 43382988 +chr1 43382988 45354942 +chr1 45354942 47326896 +chr1 47326896 49298850 +chr1 49298850 51270804 +chr1 51270804 53242758 +chr1 53242758 55214712 +chr1 55214712 57186666 +chr1 57186666 59158620 +chr1 59158620 61130574 +chr1 61130574 63102528 +chr1 63102528 65074482 +chr1 65074482 67046436 +chr1 67046436 69018390 +chr1 69018390 70990344 +chr1 70990344 72962298 +chr1 72962298 74934252 +chr1 74934252 76906206 +chr1 76906206 78878160 +chr1 78878160 80850114 +chr1 80850114 82822068 +chr1 82822068 84794022 +chr1 84794022 86765976 +chr1 86765976 88737930 +chr1 88737930 90709884 +chr1 90709884 92681838 +chr1 92681838 94653792 +chr1 94653792 96625746 +chr1 96625746 98597700 +chr1 98597700 100569654 +chr1 100569654 102541608 +chr1 102541608 104513562 +chr1 104513562 106485516 +chr1 106485516 108457470 +chr1 108457470 110429424 +chr1 110429424 112401378 +chr1 112401378 114373332 +chr1 114373332 116345286 +chr1 116345286 118317240 +chr1 118317240 120289194 +chr1 120289194 122261148 +chr1 122261148 124233102 +chr1 124233102 126205056 +chr1 126205056 128177010 +chr1 128177010 130148964 +chr1 130148964 132120918 +chr1 132120918 134092872 +chr1 134092872 136064826 +chr1 136064826 138036780 +chr1 138036780 140008734 +chr1 140008734 141980688 +chr1 141980688 143952642 +chr1 143952642 145924596 +chr1 145924596 147896550 +chr1 147896550 149868504 +chr1 149868504 151840458 +chr1 151840458 153812412 +chr1 153812412 155784366 +chr1 155784366 157756320 +chr1 157756320 159728274 +chr1 159728274 161700228 +chr1 161700228 163672182 +chr1 163672182 165644136 +chr1 165644136 167616090 +chr1 167616090 169588044 +chr1 169588044 171559998 +chr1 171559998 173531952 +chr1 173531952 175503906 +chr1 175503906 177475860 +chr1 177475860 179447814 +chr1 179447814 181419768 +chr1 181419768 183391722 +chr1 183391722 185363676 +chr1 185363676 187335630 +chr1 187335630 189307584 +chr1 189307584 191279538 +chr1 191279538 193251492 +chr1 193251492 195223446 +chr1 195223446 197195432 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 test-data/makeWindowBed_result4.bed --- a/test-data/makeWindowBed_result4.bed Mon Oct 03 07:36:08 2016 -0400 +++ b/test-data/makeWindowBed_result4.bed Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -1,45 +1,45 @@ -chr5 60000 60667 -chr5 60667 61334 -chr5 61334 62001 -chr5 62001 62668 -chr5 62668 63335 -chr5 63335 64002 -chr5 64002 64669 -chr5 64669 65336 -chr5 65336 66003 -chr5 66003 66670 -chr5 66670 67337 -chr5 67337 68004 -chr5 68004 68671 -chr5 68671 69338 -chr5 69338 70000 -chr5 73000 74134 -chr5 74134 75268 -chr5 75268 76402 -chr5 76402 77536 -chr5 77536 78670 -chr5 78670 79804 -chr5 79804 80938 -chr5 80938 82072 -chr5 82072 83206 -chr5 83206 84340 -chr5 84340 85474 -chr5 85474 86608 -chr5 86608 87742 -chr5 87742 88876 -chr5 88876 90000 -chr5 100000 100067 -chr5 100067 100134 -chr5 100134 100201 -chr5 100201 100268 -chr5 100268 100335 -chr5 100335 100402 -chr5 100402 100469 -chr5 100469 100536 -chr5 100536 100603 -chr5 100603 100670 -chr5 100670 100737 -chr5 100737 100804 -chr5 100804 100871 -chr5 100871 100938 -chr5 100938 101000 +chr5 60000 60666 +chr5 60666 61332 +chr5 61332 61998 +chr5 61998 62664 +chr5 62664 63330 +chr5 63330 63996 +chr5 63996 64662 +chr5 64662 65328 +chr5 65328 65994 +chr5 65994 66660 +chr5 66660 67326 +chr5 67326 67992 +chr5 67992 68658 +chr5 68658 69324 +chr5 69324 70000 +chr5 73000 74133 +chr5 74133 75266 +chr5 75266 76399 +chr5 76399 77532 +chr5 77532 78665 +chr5 78665 79798 +chr5 79798 80931 +chr5 80931 82064 +chr5 82064 83197 +chr5 83197 84330 +chr5 84330 85463 +chr5 85463 86596 +chr5 86596 87729 +chr5 87729 88862 +chr5 88862 90000 +chr5 100000 100066 +chr5 100066 100132 +chr5 100132 100198 +chr5 100198 100264 +chr5 100264 100330 +chr5 100330 100396 +chr5 100396 100462 +chr5 100462 100528 +chr5 100528 100594 +chr5 100594 100660 +chr5 100660 100726 +chr5 100726 100792 +chr5 100792 100858 +chr5 100858 100924 +chr5 100924 101000 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 03 07:36:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bedtools" version="2.24"> - <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 unionBedGraphs.xml --- a/unionBedGraphs.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/unionBedGraphs.xml Mon Oct 17 10:13:35 2016 -0400 |
| b |
| @@ -132,7 +132,7 @@ **Examples using the Zero Coverage checkbox** Output example (*without* checking "Report regions with zero coverage"):: - + chr1 900 1000 0 60 0 chr1 1000 1500 10 60 0 chr1 1500 1600 0 60 0 @@ -145,7 +145,7 @@ Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:: - + chr1 0 900 0 0 0 (*) chr1 900 1000 0 60 0 chr1 1000 1500 10 60 0 @@ -157,7 +157,7 @@ chr1 2050 2070 20 0 80 chr1 2070 2090 20 0 0 chr1 2090 2100 20 0 20 - chr1 2100 247249719 0 0 0 (*) + chr1 2100 247249719 0 0 0 (*) ------ @@ -167,7 +167,7 @@ The default value is '0', but you can use any other value. Output example with **filler = N/A**:: - + chr1 900 1000 N/A 60 N/A chr1 1000 1500 10 60 N/A chr1 1500 1600 N/A 60 N/A @@ -204,14 +204,14 @@ The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. Input Example:: - - File-1 File-2 + + File-1 File-2 chr1 200 300 Sample1 chr1 100 240 0.75 chr1 400 450 Sample1 chr1 250 700 0.43 chr1 530 600 Sample2 Output Example:: - + chr1 100 200 0 0.75 chr1 200 240 Sample1 0.75 chr1 240 250 Sample1 0 |
| b |
| diff -r c78cf6fe3018 -r 7308cc546a36 windowBed.xml --- a/windowBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/windowBed.xml Mon Oct 17 10:13:35 2016 -0400 |
| [ |
| @@ -9,11 +9,11 @@ <![CDATA[ bedtools window #if $inputA.ext == "bam": - -abam $inputA + -abam '$inputA' #else: - -a $inputA + -a '$inputA' #end if - -b $inputB + -b '$inputB' $bed $strandB #if $addition.addition_select == 'window': @@ -26,7 +26,7 @@ $number $nooverlaps $header - > $output + > '$output' ]]> </command> <inputs> |