| Previous changeset 3:2cd7e321d259 (2015-05-27) Next changeset 5:f8b7dc21b4ee (2016-02-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 |
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modified:
annotateBed.xml bamToBed.xml bedToBam.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml expandBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml linksBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml sortBed.xml subtractBed.xml tagBed.xml test-data/annotateBed_result.bed test-data/bedToBam_result.bam tool_dependencies.xml unionBedGraphs.xml windowBed.xml |
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added:
bamToFastq.xml spacingBed.xml test-data/closestBed_result6.bed test-data/spacingBed_result1.bed |
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| diff -r 2cd7e321d259 -r 607c0576c6ab annotateBed.xml --- a/annotateBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/annotateBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1"> + <description>annotate coverage of features from multiple files</description> <macros> <import>macros.xml</import> </macros> @@ -7,6 +7,7 @@ <expand macro="stdio" /> <command> <![CDATA[ + bedtools annotate -i "${inputA}" #if $names.names_select == 'yes': @@ -22,6 +23,8 @@ #else: #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) -files "${files}" + #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] ) + -names "${names}" #end if $strand $counts |
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| diff -r 2cd7e321d259 -r 607c0576c6ab bamToBed.xml --- a/bamToBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/bamToBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,12 +1,21 @@ -<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0"> + <description>converter</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="1.2">samtools</requirement> + </expand> <expand macro="stdio" /> <command> <![CDATA[ + + #if $input.extension == 'bam' and $option == "-bedpe": + samtools sort -n "${input}" ./input && + #else + ln -s "${input}" ./input.bam && + #end if + bedtools bamtobed $option $ed_score @@ -14,20 +23,20 @@ #if $tag and str($tag).strip(): -tag "${tag}" #end if - -i "${input}" + -i ./input.bam > "${output}" ]]> </command> <inputs> <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> <param name="option" type="select" label="What type of BED output would you like"> - <option value="">Create a 6-column BED file.</option> - <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> - <option value="-bedpe">Create a paired-end, BEDPE format.</option> + <option value="">Create a 6-column BED file</option> + <option value="-bed12">Create a full, 12-column "blocked" BED file</option> + <option value="-bedpe">Create a paired-end, BEDPE format</option> </param> <expand macro="split" /> <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false" - label="Use alignment's edit-distance for BED score" /> + label="Use alignment's edit-distance for BED score" help="(-ed)" /> <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score" help="(-tag)"/> </inputs> @@ -56,16 +65,16 @@ .. class:: infomark -The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments. +The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. +For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. +However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). +This is important for RNA-seq and structural variation experiments. .. class:: warningmark -If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0). +If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0). -.. class:: warningmark - -If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name. @REFERENCES@ ]]> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab bamToFastq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamToFastq.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -0,0 +1,39 @@ +<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command> + bedtools bamtofastq + $tags + -i '$input' + -fq '$output' + #if $fq2: + -fq2 '$output2' + #end if + </command> + <inputs> + <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/> + <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/> + <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end. + Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/> + </inputs> + <outputs> + <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/> + <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)"> + <filter>fq2 is True</filter> + </data> + </outputs> +<help> + +**What it does** + +bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format. + +@REFERENCES@ + + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab bedToBam.xml --- a/bedToBam.xml Wed May 27 12:54:35 2015 -0400 +++ b/bedToBam.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0"> + <description>converter</description> <macros> <import>macros.xml</import> </macros> @@ -31,7 +31,7 @@ <test> <param name="input" value="bedToBam1.bed" ftype="bed" /> <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <output name="output" file="bedToBam_result.bam" lines_diff="2" ftype="bam" /> + <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> </test> </tests> <help> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab bedpeToBam.xml --- a/bedpeToBam.xml Wed May 27 12:54:35 2015 -0400 +++ b/bedpeToBam.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0"> + <description>converter</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab closestBed.xml --- a/closestBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/closestBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>find the closest, potentially non-overlapping interval</description> <macros> <import>macros.xml</import> </macros> @@ -20,6 +20,9 @@ $io -mdb $mdb -t $ties + #if $k: + -k $k + #end if -a $inputA -b $inputBs > $output @@ -52,35 +55,21 @@ <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option> <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option> </param> + <when value="" /> <when value="ref"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - 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" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> <when value="a"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - 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" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> <when value="b"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - 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" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> </conditional> + <param name="k" type="integer" value="1" optional="True" min="1" + label="Report the k closest hits" help="(-k)"/> + <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" label="Ignore features in B that overlap A" help="That is, we want close, yet not touching features only. (-io)" /> @@ -126,6 +115,12 @@ <param name="addition2_select" value="a" /> <output name="output" file="closestBed_result5.bed" ftype="bed" /> </test> + <test> + <param name="inputA" value="closestBedA.bed" ftype="bed" /> + <param name="inputB" value="a.bed" ftype="bed" /> + <param name="k" value="3" /> + <output name="output" file="closestBed_result6.bed" ftype="bed" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r 2cd7e321d259 -r 607c0576c6ab clusterBed.xml --- a/clusterBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/clusterBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>cluster overlapping/nearby intervals</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab complementBed.xml --- a/complementBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/complementBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>Extract intervals not represented by an interval file</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab expandBed.xml --- a/expandBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/expandBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_expandbed" name="ExpandBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>replicate lines based on lists of values in columns</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab fisherBed.xml --- a/fisherBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/fisherBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>calculate Fisher statistic between two feature files</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab flankBed.xml --- a/flankBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/flankBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>create new intervals from the flanks of existing intervals</description> <macros> <import>macros.xml</import> </macros> @@ -27,10 +27,10 @@ <expand macro="genome" /> <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" - help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> + help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" /> <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" - help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> + help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" /> <expand macro="addition" /> </inputs> <outputs> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab genomeCoverageBed.xml --- a/genomeCoverageBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/genomeCoverageBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> - <description>in bedGraph or histogram format</description> + <description>compute the coverage over an entire genome</description> <macros> <import>macros.xml</import> </macros> @@ -74,7 +74,7 @@ label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> - <param name="five" type="boolean" checked="False" truevalue="-d" falsevalue="" + <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue="" label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab getfastaBed.xml --- a/getfastaBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/getfastaBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>use intervals to extract sequences from a FASTA file</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab groupbyBed.xml --- a/groupbyBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/groupbyBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>group by common cols and summarize other cols</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab intersectBed.xml --- a/intersectBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/intersectBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_intersectbed" name="Intersect interval files" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.0"> + <description>find overlapping intervals in various ways</description> <macros> <import>macros.xml</import> </macros> @@ -28,6 +28,7 @@ $once $header $modes + $count > "${output}" ]]> </command> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab jaccardBed.xml --- a/jaccardBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/jaccardBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_jaccard" name="JaccardBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>calculate the distribution of relative distances between two files</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab linksBed.xml --- a/linksBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/linksBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>create a HTML page of links to UCSC locations</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab macros.xml --- a/macros.xml Wed May 27 12:54:35 2015 -0400 +++ b/macros.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,11 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.22">bedtools</requirement> + <requirement type="package" version="2.24">bedtools</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.22</token> + <token name="@WRAPPER_VERSION@">2.24</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> @@ -53,6 +53,23 @@ <param format="tabular" name="genome" type="data" label="Genome file" /> <!--TODO: make use of: ${chromInfo} --> </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" + 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" + 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" + 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" + help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" /> + </xml> <xml name="addition"> <conditional name="addition"> <param name="addition_select" type="select" label="Choose what you want to do"> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab makeWindowsBed.xml --- a/makeWindowsBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/makeWindowsBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>make interval windows across a genome</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab mapBed.xml --- a/mapBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/mapBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1"> - <description></description> + <description>apply a function to a column for each overlapping interval</description> <macros> <import>macros.xml</import> </macros> @@ -41,6 +41,7 @@ <when value="-g"> <expand macro="genome" /> </when> + <when value="" /> </conditional> </inputs> <outputs> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab maskFastaBed.xml --- a/maskFastaBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/maskFastaBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>use intervals to mask sequences from a FASTA file</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab mergeBed.xml --- a/mergeBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/mergeBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1"> - <description>(mergeBed)</description> +<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.1"> + <description>combine overlapping/nearby intervals into a single interval</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab multiCov.xml --- a/multiCov.xml Wed May 27 12:54:35 2015 -0400 +++ b/multiCov.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>counts coverage from multiple BAMs at specific intervals</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab multiIntersectBed.xml --- a/multiIntersectBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/multiIntersectBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0"> - <description></description> +<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> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab nucBed.xml --- a/nucBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/nucBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>profile the nucleotide content of intervals in a FASTA file</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab overlapBed.xml --- a/overlapBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/overlapBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_overlapbed" name="OverlapBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>computes the amount of overlap from two intervals</description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 2cd7e321d259 -r 607c0576c6ab randomBed.xml --- a/randomBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/randomBed.xml Wed Jan 27 15:15:59 2016 -0500 |
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| @@ -1,5 +1,5 @@ <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>generate random intervals in a genome</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab reldist.xml --- a/reldist.xml Wed May 27 12:54:35 2015 -0400 +++ b/reldist.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_reldistbed" name="ReldistBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>calculate the distribution of relative distances</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab shuffleBed.xml --- a/shuffleBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/shuffleBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>randomly redistrubute intervals in a genome</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab slopBed.xml --- a/slopBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/slopBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>adjust the size of intervals</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab sortBed.xml --- a/sortBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/sortBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ -<tool id="bedtools_sortbed" name="Sort BED files" version="@WRAPPER_VERSION@.0"> - <description></description> +<tool id="bedtools_sortbed" name="SortBED" version="@WRAPPER_VERSION@.0"> + <description>order the intervals</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab spacingBed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spacingBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| [ |
| @@ -0,0 +1,38 @@ +<tool id="bedtools_spacingbed" name="SpacingBed" version="@WRAPPER_VERSION@.0"> + <description>reports the distances between features</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command> +<![CDATA[ + bedtools spacing + -i $input + > $output +]]> + </command> + <inputs> + <param format="bed,vcf,gff,gff3,bam" name="input" type="data" label="BED/VCF/GFF/BAM file"/> + </inputs> + <outputs> + <data format_source="input" name="output" metadata_source="input" label="Spaces between intervals of ${input}"/> + </outputs> + <tests> + <test> + <param name="input" value="a.bed" ftype="bed" /> + <output name="output" file="spacingBed_result1.bed" ftype="bed" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Report the spacing between intervals in a file. + + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab subtractBed.xml --- a/subtractBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/subtractBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>remove intervals based on overlaps</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab tagBed.xml --- a/tagBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/tagBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>tag BAM alignments based on overlaps with interval files</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab test-data/annotateBed_result.bed --- a/test-data/annotateBed_result.bed Wed May 27 12:54:35 2015 -0400 +++ b/test-data/annotateBed_result.bed Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,3 +1,4 @@ +# 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 2cd7e321d259 -r 607c0576c6ab test-data/bedToBam_result.bam |
| b |
| Binary file test-data/bedToBam_result.bam has changed |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab test-data/closestBed_result6.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closestBed_result6.bed Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +chr1 100 200 chr1 100 200 +chr1 100 200 chr1 180 250 +chr1 100 200 chr1 250 500 |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab test-data/spacingBed_result1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spacingBed_result1.bed Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +chr1 100 200 . +chr1 180 250 0 +chr1 250 500 0 +chr1 501 1000 1 |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab tool_dependencies.xml --- a/tool_dependencies.xml Wed May 27 12:54:35 2015 -0400 +++ b/tool_dependencies.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bedtools" version="2.22"> - <repository changeset_revision="960f83563956" name="package_bedtools_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bedtools" version="2.24"> + <repository changeset_revision="39b86c1e267d" 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 2cd7e321d259 -r 607c0576c6ab unionBedGraphs.xml --- a/unionBedGraphs.xml Wed May 27 12:54:35 2015 -0400 +++ b/unionBedGraphs.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>combines coverage intervals from multiple BEDGRAPH files</description> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r 2cd7e321d259 -r 607c0576c6ab windowBed.xml --- a/windowBed.xml Wed May 27 12:54:35 2015 -0400 +++ b/windowBed.xml Wed Jan 27 15:15:59 2016 -0500 |
| b |
| @@ -1,5 +1,5 @@ <tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>find overlapping intervals within a window around an interval</description> <macros> <import>macros.xml</import> </macros> |