| Previous changeset 40:a68aa6c1204a (2021-09-09) Next changeset 42:841fb4dc3ab3 (2022-01-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" |
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modified:
annotateBed.xml bamToBed.xml bed12ToBed6.xml bedToBam.xml bedToIgv.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml coverageBed.xml expandBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml linksBed.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 spacingBed.xml subtractBed.xml tagBed.xml test-data/annotateBed4.bed unionBedGraphs.xml windowBed.xml |
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added:
test-data/bamToBed_result3.bed |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b annotateBed.xml --- a/annotateBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/annotateBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>annotate coverage of features from multiple files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -66,7 +66,7 @@ <test> <param name="inputA" value="annotateBed1.bed" ftype="bed" /> <param name="names_select" value="no" /> - <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" /> + <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed"/> <output name="output" file="annotateBed_result.bed" ftype="bed" /> </test> </tests> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b bamToBed.xml --- a/bamToBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/bamToBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,16 +1,16 @@ -<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>converter</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements"> <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> </expand> <expand macro="stdio" /> <command><![CDATA[ #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": - samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input && + samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam && #else ln -s '${input}' ./input.bam && #end if @@ -54,6 +54,12 @@ <param name="tag" value="NM" /> <output name="output" file="bamToBed_result2.bed" ftype="bed" /> </test> + <test> + <param name="input" value="bedpeToBam_result1.bam" ftype="bam" /> + <param name="option" value="-bedpe" /> + <param name="tag" value="" /> + <output name="output" file="bamToBed_result3.bed" ftype="bed" /> + </test> </tests> <help><![CDATA[ **What it does** |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b bed12ToBed6.xml --- a/bed12ToBed6.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/bed12ToBed6.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>converter</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b bedToBam.xml --- a/bedToBam.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/bedToBam.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>converter</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b bedToIgv.xml --- a/bedToIgv.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/bedToIgv.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>create batch script for taking IGV screenshots</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b bedpeToBam.xml --- a/bedpeToBam.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/bedpeToBam.xml Thu Nov 04 11:36:55 2021 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>converter</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> --> <requirements> <requirement type="package" version="2.27.1">bedtools</requirement> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b closestBed.xml --- a/closestBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/closestBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>find the closest, potentially non-overlapping interval</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b clusterBed.xml --- a/clusterBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/clusterBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>cluster overlapping/nearby intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b complementBed.xml --- a/complementBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/complementBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>Extract intervals not represented by an interval file</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -23,7 +23,7 @@ <test> <param name="input" value="a.bed" ftype="bed" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" /> + <param name="genome" value="mm9_chr1.len" ftype="tabular" /> <output name="output" file="complementBed_result1.bed" ftype="bed" /> </test> </tests> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b coverageBed.xml --- a/coverageBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/coverageBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| b |
| @@ -1,9 +1,9 @@ <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>of features in file B on the features in file A (bedtools coverage)</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements"> <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> </expand> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b expandBed.xml --- a/expandBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/expandBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>replicate lines based on lists of values in columns</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b fisherBed.xml --- a/fisherBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/fisherBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>calculate Fisher statistic between two feature files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b flankBed.xml --- a/flankBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/flankBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>create new intervals from the flanks of existing intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -39,7 +39,7 @@ <test> <param name="input" value="a.bed" ftype="bed" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len"/> + <param name="genome" value="mm9_chr1.len" ftype="tabular"/> <param name="addition_select" value="b"/> <param name="b" value="5"/> <output name="output" file="flankBed_result1.bed" ftype="bed" /> @@ -47,7 +47,7 @@ <test> <param name="input" value="a.bed" ftype="bed" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len"/> + <param name="genome" value="mm9_chr1.len" ftype="tabular"/> <param name="addition_select" value="lr"/> <param name="l" value="2"/> <param name="r" value="3"/> |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b genomeCoverageBed.xml --- a/genomeCoverageBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/genomeCoverageBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>compute the coverage over an entire genome</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b getfastaBed.xml --- a/getfastaBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/getfastaBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>use intervals to extract sequences from a FASTA file</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b groupbyBed.xml --- a/groupbyBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/groupbyBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>group by common cols and summarize other cols</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -25,7 +25,7 @@ </sanitizer> </param> <param name="operation" argument="-o" type="select" label="Specify the operation"> - <option value="sum" selected="true">Sum - numeric only</option> + <!-- <option value="sum" selected="true">Sum - numeric only</option> This is already in math--> <option value="stdev">Stdev - numeric only</option> <option value="sstdev">Sstdev - numeric only</option> <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option> |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b intersectBed.xml --- a/intersectBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/intersectBed.xml Thu Nov 04 11:36:55 2021 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>find overlapping intervals in various ways</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements"> <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> </expand> |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b jaccardBed.xml --- a/jaccardBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/jaccardBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>calculate the distribution of relative distances between two files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b linksBed.xml --- a/linksBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/linksBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>create a HTML page of links to UCSC locations</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b makeWindowsBed.xml --- a/makeWindowsBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/makeWindowsBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>make interval windows across a genome</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b mapBed.xml --- a/mapBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/mapBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@"> <description>apply a function to a column for each overlapping interval</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b maskFastaBed.xml --- a/maskFastaBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/maskFastaBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>use intervals to mask sequences from a FASTA file</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b mergeBed.xml --- a/mergeBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/mergeBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>combine overlapping/nearby intervals into a single interval</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b multiCov.xml --- a/multiCov.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/multiCov.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>counts coverage from multiple BAMs at specific intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b multiIntersectBed.xml --- a/multiIntersectBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/multiIntersectBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>identifies common intervals among multiple interval files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -86,7 +86,7 @@ <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> <param name="empty_selector" value="-empty" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="multiIntersectBed1.len" /> + <param name="genome" value="multiIntersectBed1.len" ftype="tabular" /> <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> </test> </tests> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b nucBed.xml --- a/nucBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/nucBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>profile the nucleotide content of intervals in a FASTA file</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b overlapBed.xml --- a/overlapBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/overlapBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>computes the amount of overlap from two intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b randomBed.xml --- a/randomBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/randomBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>generate random intervals in a genome</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -28,7 +28,7 @@ <tests> <test> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" /> + <param name="genome" value="mm9_chr1.len" ftype="tabular" /> <param name="seed_choose" value="False" /> <param name="length" value="5" /> <param name="intervals" value="3" /> |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b reldist.xml --- a/reldist.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/reldist.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>calculate the distribution of relative distances</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b shuffleBed.xml --- a/shuffleBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/shuffleBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>randomly redistrubute intervals in a genome</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b slopBed.xml --- a/slopBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/slopBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>adjust the size of intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a68aa6c1204a -r 7ab85ac5f64b sortBed.xml --- a/sortBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/sortBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>order the intervals</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b spacingBed.xml --- a/spacingBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/spacingBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>reports the distances between features</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b subtractBed.xml --- a/subtractBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/subtractBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>remove intervals based on overlaps</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b tagBed.xml --- a/tagBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/tagBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>tag BAM alignments based on overlaps with interval files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b test-data/annotateBed4.bed --- a/test-data/annotateBed4.bed Thu Sep 09 13:04:07 2021 +0000 +++ b/test-data/annotateBed4.bed Thu Nov 04 11:36:55 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -chr1 0 120 known1 - -chr1 150 160 known2 - -chr2 0 10000 known3 + +chr1 0 120 known 1 - +chr1 150 160 known 2 - +chr2 0 10000 known 3 + |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b test-data/bamToBed_result3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamToBed_result3.bed Thu Nov 04 11:36:55 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +chr1 100 200 chr5 5000 5100 bedpe_example1 255 + - +chr9 1000 5000 chr9 3000 3800 bedpe_example2 255 + - |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b unionBedGraphs.xml --- a/unionBedGraphs.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/unionBedGraphs.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>combines coverage intervals from multiple BEDGRAPH files</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ @@ -83,26 +83,26 @@ <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> <param name="empty_selector" value="-empty" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="unionBedGraphs1.len" /> + <param name="genome" value="unionBedGraphs1.len" ftype="tabular" /> <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> </test> <test> <param name="tag_select" value="custom" /> <repeat name="bedgraphs"> - <param name="input" value="unionBedGraphs1.bg" /> + <param name="input" value="unionBedGraphs1.bg" ftype="bedgraph" /> <param name="custom_name" value="first" /> </repeat> <repeat name="bedgraphs"> - <param name="input" value="unionBedGraphs2.bg" /> + <param name="input" value="unionBedGraphs2.bg" ftype="bedgraph" /> <param name="custom_name" value="second" /> </repeat> <repeat name="bedgraphs"> - <param name="input" value="unionBedGraphs3.bg" /> + <param name="input" value="unionBedGraphs3.bg" ftype="bedgraph" /> <param name="custom_name" value="third" /> </repeat> <param name="empty_selector" value="-empty" /> <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="unionBedGraphs1.len" /> + <param name="genome" value="unionBedGraphs1.len" ftype="tabular" /> <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> </test> </tests> |
| b |
| diff -r a68aa6c1204a -r 7ab85ac5f64b windowBed.xml --- a/windowBed.xml Thu Sep 09 13:04:07 2021 +0000 +++ b/windowBed.xml Thu Nov 04 11:36:55 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>find overlapping intervals within a window around an interval</description> - <expand macro="bio_tools" /> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ |