| Previous changeset 45:a1a923cd89e8 (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4 |
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modified:
bamToBed.xml bedToBam.xml bedpeToBam.xml complementBed.xml coverageBed.xml fisherBed.xml flankBed.xml getfastaBed.xml intersectBed.xml jaccardBed.xml macros.xml randomBed.xml shuffleBed.xml slopBed.xml sortBed.xml |
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added:
test-data/jaccardBed_strand_result2.bed |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c bamToBed.xml --- a/bamToBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/bamToBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,11 +1,11 @@ -<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>converter</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements"> - <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> + <requirement type="package" version="1.18">samtools</requirement> </expand> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c bedToBam.xml --- a/bedToBam.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/bedToBam.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>converter</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c bedpeToBam.xml --- a/bedpeToBam.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/bedpeToBam.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>converter</description> <macros> <import>macros.xml</import> @@ -6,7 +6,7 @@ <expand macro="bio_tools" /> <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> --> <requirements> - <requirement type="package" version="2.27.1">bedtools</requirement> + <requirement type="package" version="2.31.1">bedtools</requirement> </requirements> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c complementBed.xml --- a/complementBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/complementBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,11 +1,11 @@ -<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Extract intervals not represented by an interval file</description> <macros> <import>macros.xml</import> </macros> - <expand macro="bio_tools" /> - <expand macro="requirements" /> - <expand macro="stdio" /> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ complementBed -i '$input' @@ -14,17 +14,17 @@ ]]></command> <inputs> <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> - <expand macro="input_conditional_genome_file" /> + <expand macro="input_conditional_genome_file"/> </inputs> <outputs> <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/> </outputs> <tests> <test> - <param name="input" value="a.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <output name="output" file="complementBed_result1.bed" ftype="bed" /> + <param name="input" value="a.bed" ftype="bed"/> + <param name="genome_file_opts_selector" value="hist"/> + <param name="genome" value="mm9_chr1.len" ftype="tabular"/> + <output name="output" file="complementBed_result1.bed" ftype="bed"/> </test> </tests> <help><![CDATA[ @@ -36,5 +36,5 @@ @REFERENCES@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c coverageBed.xml --- a/coverageBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/coverageBed.xml Sat May 18 23:28:38 2024 +0000 |
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| b'@@ -1,13 +1,13 @@\n-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">\n+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">\n <description>of features in file B on the features in file A (bedtools coverage)</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="bio_tools" />\n+ <expand macro="bio_tools"/>\n <expand macro="requirements">\n- <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>\n+ <requirement type="package" version="1.18">samtools</requirement>\n </expand>\n- <expand macro="stdio" />\n+ <expand macro="stdio"/>\n <command><![CDATA[\n bedtools coverage\n $d\n@@ -41,95 +41,83 @@\n > \'$output\'\n ]]></command>\n <inputs>\n- <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />\n+ <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>\n <conditional name="reduce_or_iterate">\n <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">\n <option value="iterate" selected="true">One output file per \'input B\' file</option>\n <option value="reduce">Single output containing results for all \'input B\' files</option>\n </param>\n <when value="iterate">\n- <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"\n- label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>\n+ <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>\n </when>\n <when value="reduce">\n- <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"\n- label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>\n+ <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" multiple="true"/>\n </when>\n </conditional>\n- <expand macro="split" />\n- <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"\n- help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>\n- <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"\n- label="Report the depth at each position in each A feature"\n- help="Positions reported are one based. Each position and depth follow the complete B feature" />\n- <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"\n- label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"\n- help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />\n- <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"\n- help="Report the mean depth of all positions in each A feature."/>\n- <expand macro="overlap" name="overlap_a" />\n- <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />\n- <param nam'..b' <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="multiCov1.bed" ftype="bed" />\n- <param name="reduce_or_iterate_selector" value="reduce" />\n- <param name="inputB" value="srma_in3.bam" ftype="bam" />\n+ <param name="inputA" value="multiCov1.bed" ftype="bed"/>\n+ <param name="reduce_or_iterate_selector" value="reduce"/>\n+ <param name="inputB" value="srma_in3.bam" ftype="bam"/>\n <param name="sorted" value="true"/>\n- <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />\n+ <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="coverageBedA.bed" ftype="bed" />\n- <param name="inputB" value="coverageBedB.bed" ftype="bed" />\n- <param name="overlap_b" value="1" />\n- <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />\n+ <param name="inputA" value="coverageBedA.bed" ftype="bed"/>\n+ <param name="inputB" value="coverageBedB.bed" ftype="bed"/>\n+ <param name="overlap_b" value="1"/>\n+ <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="coverageBedA.bed" ftype="bed" />\n- <param name="inputB" value="coverageBedB.bed" ftype="bed" />\n- <param name="overlap_a" value="1E-5" />\n- <param name="reciprocal_overlap" value="true" />\n- <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />\n+ <param name="inputA" value="coverageBedA.bed" ftype="bed"/>\n+ <param name="inputB" value="coverageBedB.bed" ftype="bed"/>\n+ <param name="overlap_a" value="1E-5"/>\n+ <param name="reciprocal_overlap" value="true"/>\n+ <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="multiCov1.bed" ftype="bed" />\n- <param name="reduce_or_iterate_selector" value="reduce" />\n- <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />\n+ <param name="inputA" value="multiCov1.bed" ftype="bed"/>\n+ <param name="reduce_or_iterate_selector" value="reduce"/>\n+ <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>\n <param name="sorted" value="true"/>\n- <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />\n+ <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="coverageBedA2.bed" ftype="bed" />\n- <param name="inputB" value="coverageBed.bam" ftype="bam" />\n- <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />\n+ <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>\n+ <param name="inputB" value="coverageBed.bam" ftype="bam"/>\n+ <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>\n </test>\n <test>\n- <param name="inputA" value="coverageBedA2.bed" ftype="bed" />\n- <param name="inputB" value="coverageBed.bam" ftype="bam" />\n+ <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>\n+ <param name="inputB" value="coverageBed.bam" ftype="bam"/>\n <param name="mean" value="true"/>\n- <output name="output" file="mean_coverage.bed" ftype="bed" />\n+ <output name="output" file="mean_coverage.bed" ftype="bed"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -155,5 +143,5 @@\n \n @REFERENCES@\n ]]></help>\n- <expand macro="citations" />\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c fisherBed.xml --- a/fisherBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/fisherBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>calculate Fisher statistic between two feature files</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c flankBed.xml --- a/flankBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/flankBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>create new intervals from the flanks of existing intervals</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c getfastaBed.xml --- a/getfastaBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/getfastaBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>use intervals to extract sequences from a FASTA file</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c intersectBed.xml --- a/intersectBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/intersectBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,11 +1,11 @@ -<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>find overlapping intervals in various ways</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements"> - <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> + <requirement type="package" version="1.18">samtools</requirement> </expand> <expand macro="stdio" /> <command><![CDATA[ |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c jaccardBed.xml --- a/jaccardBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/jaccardBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="bio_tools" /> - <expand macro="requirements" /> - <expand macro="stdio" /> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ bedtools jaccard $strand @@ -22,29 +22,33 @@ <inputs> <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> - <expand macro="overlap" /> + <expand macro="overlap"/> <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> - <expand macro="reciprocal" /> - <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" - 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." /> - <expand macro="strand2" /> - <expand macro="split" /> + <expand macro="reciprocal"/> + <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" 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."/> + <expand macro="split"/> </inputs> <outputs> - <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" /> + <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/> </outputs> <tests> <test> - <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> - <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> - <output name="output" file="jaccardBed_result1.bed" ftype="bed" /> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <output name="output" file="jaccardBed_result1.bed" ftype="bed"/> </test> <test> - <param name="inputA" value="jaccardBed1.bed" ftype="bed" /> - <param name="inputB" value="jaccardBed2.bed" ftype="bed" /> - <param name="overlap" value="0.1" /> - <output name="output" file="jaccardBed_result2.bed" ftype="bed" /> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <param name="overlap" value="0.1"/> + <output name="output" file="jaccardBed_result2.bed" ftype="bed"/> + </test> + <test> + <param name="inputA" value="jaccardBed1.bed" ftype="bed"/> + <param name="inputB" value="jaccardBed2.bed" ftype="bed"/> + <param name="overlap" value="0.1"/> + <param name="strand" value="true"/> + <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/> </test> </tests> <help><![CDATA[ @@ -61,5 +65,5 @@ @REFERENCES@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c macros.xml --- a/macros.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/macros.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -10,7 +10,7 @@ <xref type="bio.tools">bedtools</xref> </xrefs> </xml> - <token name="@TOOL_VERSION@">2.30.0</token> + <token name="@TOOL_VERSION@">2.31.1</token> <token name="@SAMTOOLS_VERSION@">1.9</token> <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token> <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c randomBed.xml --- a/randomBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/randomBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>generate random intervals in a genome</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c shuffleBed.xml --- a/shuffleBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/shuffleBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>randomly redistrubute intervals in a genome</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c slopBed.xml --- a/slopBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/slopBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>adjust the size of intervals</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c sortBed.xml --- a/sortBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/sortBed.xml Sat May 18 23:28:38 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>order the intervals</description> <macros> <import>macros.xml</import> |
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| diff -r a1a923cd89e8 -r 64e2edfe7a2c test-data/jaccardBed_strand_result2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jaccardBed_strand_result2.bed Sat May 18 23:28:38 2024 +0000 |
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| @@ -0,0 +1,2 @@ +intersection union jaccard n_intersections +0 0 -nan 0 |