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Updating tools/bedtools from version 2.30.0 to 2.31.1 (#5303)
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* Updating tools/bedtools from version 2.30.0 to 2.31.0

* Updating tools/bedtools from version 2.31.0 to 2.31.1

* reformat and test fixes

* add test data

---------

Co-authored-by: planemo-autoupdate <[email protected]>
Co-authored-by: Bjoern Gruening <[email protected]>
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@bgruening
3 people authored May 18, 2024
1 parent 99c10c3 commit 3e7bf5a
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Showing 16 changed files with 97 additions and 103 deletions.
4 changes: 2 additions & 2 deletions tools/bedtools/bamToBed.xml
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<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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2 changes: 1 addition & 1 deletion tools/bedtools/bedToBam.xml
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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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4 changes: 2 additions & 2 deletions tools/bedtools/bedpeToBam.xml
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@@ -1,12 +1,12 @@
<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>
</macros>
<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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20 changes: 10 additions & 10 deletions tools/bedtools/complementBed.xml
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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'
Expand All @@ -14,17 +14,17 @@ complementBed
]]></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[
Expand All @@ -36,5 +36,5 @@ bedtools complement returns all intervals in a genome that are not covered by at
@REFERENCES@
]]></help>
<expand macro="citations" />
<expand macro="citations"/>
</tool>
106 changes: 47 additions & 59 deletions tools/bedtools/coverageBed.xml
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@@ -1,13 +1,13 @@
<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<description>of features in file B on the features in file A (bedtools coverage)</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools" />
<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" />
<expand macro="stdio"/>
<command><![CDATA[
bedtools coverage
$d
Expand Down Expand Up @@ -41,95 +41,83 @@ $a_or_b
> '$output'
]]></command>
<inputs>
<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" />
<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"/>
<conditional name="reduce_or_iterate">
<param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
<option value="iterate" selected="true">One output file per 'input B' file</option>
<option value="reduce">Single output containing results for all 'input B' files</option>
</param>
<when value="iterate">
<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"/>
<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"/>
</when>
<when value="reduce">
<param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
<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"/>
</when>
</conditional>
<expand macro="split" />
<param name="strandedness" argument="-s" 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"/>
<param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
label="Report the depth at each position in each A feature"
help="Positions reported are one based. Each position and depth follow the complete B feature" />
<param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
<param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
help="Report the mean depth of all positions in each A feature."/>
<expand macro="overlap" name="overlap_a" />
<expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
<param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
label="Require that the fraction overlap be reciprocal for A AND B."
help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
<param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
label="Require that the minimum fraction be satisfied for A OR B."
help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied" />
<expand macro="split"/>
<param name="strandedness" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
<param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Report the depth at each position in each A feature" help="Positions reported are one based. Each position and depth follow the complete B feature"/>
<param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth"/>
<param argument="-mean" type="boolean" truevalue="-mean" falsevalue="" checked="false" label="Mean depth" help="Report the mean depth of all positions in each A feature."/>
<expand macro="overlap" name="overlap_a"/>
<expand macro="overlap" name="overlap_b" argument="-F" fracof="B"/>
<param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Require that the fraction overlap be reciprocal for A AND B." help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B"/>
<param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Require that the minimum fraction be satisfied for A OR B." help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied"/>
<!-- -sorted -g -->
<expand macro="sorted" />
<expand macro="sorted"/>
</inputs>
<outputs>
<data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
</outputs>
<tests>
<test>
<param name="inputA" value="coverageBedA.bed" ftype="bed" />
<param name="inputB" value="coverageBedB.bed" ftype="bed" />
<output name="output" file="coverageBed_result1.bed" ftype="bed" />
<param name="inputA" value="coverageBedA.bed" ftype="bed"/>
<param name="inputB" value="coverageBedB.bed" ftype="bed"/>
<output name="output" file="coverageBed_result1.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="multiCov1.bed" ftype="bed" />
<param name="inputB" value="srma_in3.bam" ftype="bam" />
<param name="inputA" value="multiCov1.bed" ftype="bed"/>
<param name="inputB" value="srma_in3.bam" ftype="bam"/>
<param name="sorted" value="true"/>
<output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
<output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="multiCov1.bed" ftype="bed" />
<param name="reduce_or_iterate_selector" value="reduce" />
<param name="inputB" value="srma_in3.bam" ftype="bam" />
<param name="inputA" value="multiCov1.bed" ftype="bed"/>
<param name="reduce_or_iterate_selector" value="reduce"/>
<param name="inputB" value="srma_in3.bam" ftype="bam"/>
<param name="sorted" value="true"/>
<output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
<output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="coverageBedA.bed" ftype="bed" />
<param name="inputB" value="coverageBedB.bed" ftype="bed" />
<param name="overlap_b" value="1" />
<output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
<param name="inputA" value="coverageBedA.bed" ftype="bed"/>
<param name="inputB" value="coverageBedB.bed" ftype="bed"/>
<param name="overlap_b" value="1"/>
<output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="coverageBedA.bed" ftype="bed" />
<param name="inputB" value="coverageBedB.bed" ftype="bed" />
<param name="overlap_a" value="1E-5" />
<param name="reciprocal_overlap" value="true" />
<output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
<param name="inputA" value="coverageBedA.bed" ftype="bed"/>
<param name="inputB" value="coverageBedB.bed" ftype="bed"/>
<param name="overlap_a" value="1E-5"/>
<param name="reciprocal_overlap" value="true"/>
<output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="multiCov1.bed" ftype="bed" />
<param name="reduce_or_iterate_selector" value="reduce" />
<param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
<param name="inputA" value="multiCov1.bed" ftype="bed"/>
<param name="reduce_or_iterate_selector" value="reduce"/>
<param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>
<param name="sorted" value="true"/>
<output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
<output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="coverageBedA2.bed" ftype="bed" />
<param name="inputB" value="coverageBed.bam" ftype="bam" />
<output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
<param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
<param name="inputB" value="coverageBed.bam" ftype="bam"/>
<output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>
</test>
<test>
<param name="inputA" value="coverageBedA2.bed" ftype="bed" />
<param name="inputB" value="coverageBed.bam" ftype="bam" />
<param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
<param name="inputB" value="coverageBed.bam" ftype="bam"/>
<param name="mean" value="true"/>
<output name="output" file="mean_coverage.bed" ftype="bed" />
<output name="output" file="mean_coverage.bed" ftype="bed"/>
</test>
</tests>
<help><![CDATA[
Expand All @@ -155,5 +143,5 @@ The lines in the output will be comprised of each interval in A, followed by:
@REFERENCES@
]]></help>
<expand macro="citations" />
<expand macro="citations"/>
</tool>
2 changes: 1 addition & 1 deletion tools/bedtools/fisherBed.xml
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<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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2 changes: 1 addition & 1 deletion tools/bedtools/flankBed.xml
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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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2 changes: 1 addition & 1 deletion tools/bedtools/getfastaBed.xml
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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>
Expand Down
4 changes: 2 additions & 2 deletions tools/bedtools/intersectBed.xml
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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[
Expand Down
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