Mercurial > repos > iuc > bedtools
changeset 64:f6c88d2e9ae5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
| author | iuc |
|---|---|
| date | Fri, 21 Feb 2025 21:38:34 +0000 |
| parents | 7411007544bf |
| children | |
| files | annotateBed.xml bamToBed.xml bedToBam.xml bedpeToBam.xml closestBed.xml complementBed.xml coverageBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml macros.xml makeWindowsBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml randomBed.xml shuffleBed.xml slopBed.xml sortBed.xml test-data/jaccardBed_strand_result2.bed unionBedGraphs.xml windowBed.xml |
| diffstat | 26 files changed, 298 insertions(+), 284 deletions(-) [+] |
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--- a/annotateBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/annotateBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -65,8 +65,8 @@ <tests> <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="names|names_select" value="no" /> + <param name="names|beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed"/> <output name="output" file="annotateBed_result.bed" ftype="bed" /> </test> </tests>
--- a/bamToBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/bamToBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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[
--- a/bedToBam.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/bedToBam.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -29,8 +29,8 @@ <tests> <test> <param name="input" value="bedToBam1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" /> <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> </test> </tests>
--- a/bedpeToBam.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/bedpeToBam.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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[ @@ -28,8 +28,8 @@ <tests> <test> <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9.len"/> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9.len"/> <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" /> </test> </tests>
--- a/closestBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/closestBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>find the closest, potentially non-overlapping interval</description> <macros> <import>macros.xml</import> @@ -14,6 +14,8 @@ -D $addition2.addition2_select $addition2.iu $addition2.id + $addition2.fu + $addition2.fd #end if $io -mdb $mdb @@ -109,50 +111,50 @@ <tests> <test> <param name="inputA" value="closestBedA.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBedB.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBedB.bed" ftype="bed" /> <output name="output" file="closestBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_a.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> <param name="addition" value="true" /> <output name="output" file="closestBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_a.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> <param name="addition" value="True" /> <param name="mdb" value="all" /> <output name="output" file="closestBed_result3.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_c.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_d.bed" ftype="bed" /> - <param name="addition2_select" value="ref" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" /> + <param name="addition2|addition2_select" value="ref" /> <output name="output" file="closestBed_result4.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBed_c.bed" ftype="bed" /> - <param name="source" value="history" /> - <param name="inputB" value="closestBed_d.bed" ftype="bed" /> - <param name="addition2_select" value="a" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" /> + <param name="addition2|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="source" value="history" /> - <param name="inputB" value="a.bed" ftype="bed" /> + <param name="overlap_with|source" value="history" /> + <param name="overlap_with|inputB" value="a.bed" ftype="bed" /> <param name="k" value="3" /> <output name="output" file="closestBed_result6.bed" ftype="bed" /> </test> <test> <param name="inputA" value="closestBedA.bed" ftype="bed" /> - <param name="source" value="data_table" /> - <param name="inputB" value="testid" /> + <param name="overlap_with|source" value="data_table" /> + <param name="overlap_with|table" value="testid" /> <param name="k" value="3" /> <output name="output" file="closestBed_result6.bed" ftype="bed" /> </test>
--- a/complementBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/complementBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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|genome_file_opts_selector" value="hist"/> + <param name="genome_file_opts|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>
--- a/coverageBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/coverageBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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 $d @@ -41,95 +41,83 @@ > '$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="reduce_or_iterate|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="reduce_or_iterate|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|reduce_or_iterate_selector" value="reduce"/> + <param name="reduce_or_iterate|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="reduce_or_iterate|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="reduce_or_iterate|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|reduce_or_iterate_selector" value="reduce"/> + <param name="reduce_or_iterate|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="reduce_or_iterate|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="reduce_or_iterate|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[ @@ -155,5 +143,5 @@ @REFERENCES@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>
--- a/fisherBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/fisherBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -36,8 +36,8 @@ <test> <param name="inputA" value="fisherBed1.bed" ftype="bed" /> <param name="inputB" value="fisherBed2.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="fisherBed.len" ftype="tabular" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="fisherBed.len" ftype="tabular" /> <output name="output" file="fisherBed_result1.bed" ftype="bed" /> </test> </tests>
--- a/flankBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/flankBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -38,19 +38,19 @@ <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"/> - <param name="addition_select" value="b"/> - <param name="b" value="5"/> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/> + <param name="addition|addition_select" value="b"/> + <param name="addition|b" value="5"/> <output name="output" file="flankBed_result1.bed" ftype="bed" /> </test> <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"/> - <param name="addition_select" value="lr"/> - <param name="l" value="2"/> - <param name="r" value="3"/> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/> + <param name="addition|addition_select" value="lr"/> + <param name="addition|l" value="2"/> + <param name="addition|r" value="3"/> <output name="output" file="flankBed_result2.bed" ftype="bed" /> </test> </tests>
--- a/genomeCoverageBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/genomeCoverageBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -90,11 +90,11 @@ </outputs> <tests> <test> - <param name="input_type_select" value="bed" /> - <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> - <param name="report_select" value="hist" /> + <param name="input_type|input_type_select" value="bed" /> + <param name="input_type|input" value="genomeCoverageBed1.bed" ftype="bed" /> + <param name="input_type|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="input_type|genome_file_opts|genome" value="genomeCoverageBed1.len" ftype="tabular" /> + <param name="report|report_select" value="hist" /> <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> </test> </tests>
--- a/getfastaBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/getfastaBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -61,7 +61,7 @@ <tests> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> - <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="False" /> <param name="split" value="False" /> <param name="nameOnly" value="False" /> @@ -69,7 +69,7 @@ </test> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> - <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="True" /> <param name="split" value="False" /> <param name="nameOnly" value="False" /> @@ -77,7 +77,7 @@ </test> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> - <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="False" /> <param name="split" value="False" /> <param name="name" value="True" /> @@ -85,7 +85,7 @@ </test> <test> <param name="input" value="nucBed2.bed" ftype="bed" /> - <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="False" /> <param name="split" value="False" /> <param name="nameOnly" value="True" /> @@ -93,8 +93,8 @@ </test> <test> <param name="input" value="nucBed2.bed" ftype="bed" /> - <param name="fasta_source_selector" value="preloaded"/> - <param name="fasta_id" value="testid" /> + <param name="fasta_source|fasta_source_selector" value="preloaded"/> + <param name="fasta_source|fasta_id" value="testid" /> <param name="tab" value="False" /> <param name="split" value="False" /> <param name="nameOnly" value="True" />
--- a/groupbyBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/groupbyBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>group by common cols and summarize other cols</description> <macros> <import>macros.xml</import> @@ -25,13 +25,8 @@ </sanitizer> </param> <param name="operation" argument="-o" type="select" label="Specify the operation"> - <!-- <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> <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option> - <option value="first">First - numeric or text</option> - <option value="last">Last - numeric or text</option> <expand macro="math_options" /> <expand macro="additional_math_options" /> </param>
--- a/intersectBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/intersectBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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[ @@ -93,13 +93,13 @@ <expand macro="overlap" /> <conditional name="reciprocal_cond"> <expand macro="reciprocal" /> - <when value="-r"/> - <when value=""> - <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> - <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" - label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/> - </when> - </conditional> + <when value="-r"/> + <when value=""> + <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> + <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" + label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/> + </when> + </conditional> </when> </conditional> <!-- -v --> @@ -157,7 +157,6 @@ <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" /> </test> <test> - <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> <param name="inputA" value="intersect-query.bed" ftype="bed" /> <conditional name="reduce_or_iterate"> <param name="reduce_or_iterate_selector" value="reduce" /> @@ -174,7 +173,7 @@ <param name="reduce_or_iterate_selector" value="reduce" /> <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> </conditional> - <param name="invert" value="-v" /> + <param name="invert" value="true" /> <param name="sorted" value="true" /> <output name="output" file="intersect-multiple-invert.bed" ftype="bed" /> </test> @@ -252,7 +251,7 @@ <param name="reduce_or_iterate_selector" value="iterate" /> <param name="inputB" value="intersect-B.bed" ftype="bed" /> </conditional> - <param name="once" value="-u" /> + <param name="once" value="true" /> <output name="output" file="intersect-unique.bed" ftype="bed" /> </test> <test> @@ -261,7 +260,7 @@ <param name="reduce_or_iterate_selector" value="iterate" /> <param name="inputB" value="intersect-B.bed" ftype="bed" /> </conditional> - <param name="count" value="-c"/> + <param name="count" value="true"/> <output name="output" file="intersect-count.bed" ftype="bed" /> </test> <test> @@ -270,7 +269,7 @@ <param name="reduce_or_iterate_selector" value="iterate" /> <param name="inputB" value="intersect-B.bed" ftype="bed" /> </conditional> - <param name="invert" value="-v"/> + <param name="invert" value="true"/> <output name="output" file="intersect-invert.bed" ftype="bed" /> </test> <test> @@ -330,7 +329,7 @@ <param name="overlap" value="0.5" /> <conditional name="reciprocal_cond"> <param name="overlapB" value="0.5" /> - <param name="disjoint" value="-e" /> + <param name="disjoint" value="true" /> </conditional> </conditional> <output name="output" file="intersect-fracA.bed" ftype="bed" /> @@ -338,21 +337,27 @@ <!-- old tests --> <test> <param name="inputA" value="intersectBed1.bed" ftype="bed" /> - <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + <conditional name="reduce_or_iterate"> + <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + </conditional> <param name="overlap_mode" value="-wa" /> <param name="split" value="False" /> <output name="output" file="intersectBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="intersectBed1.bed" ftype="bed" /> - <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + <conditional name="reduce_or_iterate"> + <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + </conditional> <param name="overlap_mode" value="-wa,-wb" /> <param name="split" value="False" /> <output name="output" file="intersectBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="intersectBed1.bed" ftype="bed" /> - <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + <conditional name="reduce_or_iterate"> + <param name="inputB" value="intersectBed2.bed" ftype="bed" /> + </conditional> <param name="invert" value="True" /> <param name="split" value="False" /> <output name="output" file="intersectBed_result3.bed" ftype="bed" />
--- a/jaccardBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/jaccardBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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>
--- a/macros.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/macros.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -51,16 +51,7 @@ </param> </xml> <xml name="seed"> - <conditional name="seed"> - <param name="seed_choose" type="select" label="Choose Seed?"> - <option value="False" selected="true">Random Shuffling</option> - <option value="True">Choose fixed seed</option> - </param> - <when value="True"> - <param argument="-seed" type="integer" value="12345" label="Enter Seed" /> - </when> - <when value="False" /> - </conditional> + <param argument="-seed" type="integer" value="" min="0" optional="true" label="Seed" help="For reproducible 'randomness'"/> </xml> <xml name="split"> <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false" @@ -215,13 +206,19 @@ <option value="median">Median - numeric only</option> <option value="mode">Mode - numeric only</option> <option value="antimode">Antimode - numeric only</option> + <option value="stdev">Standard deviation - numeric only</option> + <option value="sstdev">Sample standard deviation - numeric only</option> <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option> </xml> <xml name="additional_math_options"> <option value="count">Count - numeric or text</option> <option value="count_disctinct">Count Distinct - numeric or text</option> <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> - <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> + <option value="distinct_sort_num">distinct sorted numerially (i.e., print a comma separated list) - numeric</option> + <option value="distinct_sort_num_desc">distinct sorted numerially descending (i.e., print a comma separated list) - numeric</option> + <option value="distinct_only">delimited list of only unique values - numeric or text</option> + <option value="first">just the first value in the column - numeric or text</option> + <option value="last">just the last value in the column - numeric or text</option> </xml> <xml name="sorted"> <!-- -sorted -g -->
--- a/makeWindowsBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/makeWindowsBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>make interval windows across a genome</description> <macros> <import>macros.xml</import> @@ -15,8 +15,8 @@ #end if #if $action.action_select == 'windowsize': -w $action.windowsize - #if $action.step_size.step_size_select == 'yes': - -s $action.step_size.step_size + #if $action.step_size != '': + -s $action.step_size #end if #else: -n $action.number @@ -46,18 +46,7 @@ <param name="windowsize" argument="-w" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows" help="i.e. same number of nucleotide in each window" /> - <conditional name="step_size"> - <param name="step_size_select" type="select" - label="Specify Step size? i.e. how many base pairs to step before creating a new window" - help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."> - <option value="yes">Yes</option> - <option value="no" selected="true">No</option> - </param> - <when value="yes"> - <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" /> - </when> - <when value="no" /> - </conditional> + <param name="step_size" argument="-s" type="integer" value="" optional="true" label="Step size" help="How many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."/> </when> <when value="number"> <param name="number" argument="-n" type="integer" value="1" @@ -77,36 +66,35 @@ </outputs> <tests> <test> - <param name="type_select" value="genome" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <param name="action_select" value="windowsize" /> - <param name="windowsize" value="1000000" /> + <param name="type|type_select" value="genome" /> + <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" /> + <param name="action|action_select" value="windowsize" /> + <param name="action|windowsize" value="1000000" /> <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> </test> <test> - <param name="type_select" value="genome" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <param name="action_select" value="windowsize" /> - <param name="windowsize" value="1000000" /> - <param name="step_size_select" value="yes" /> - <param name="step_size" value="50000" /> + <param name="type|type_select" value="genome" /> + <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" /> + <param name="action|action_select" value="windowsize" /> + <param name="action|windowsize" value="1000000" /> + <param name="action|step_size" value="50000" /> <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> </test> <test> - <param name="type_select" value="genome" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <param name="action_select" value="number" /> - <param name="number" value="100" /> + <param name="type|type_select" value="genome" /> + <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" /> + <param name="action|action_select" value="number" /> + <param name="action|number" value="100" /> <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> </test> <test> - <param name="type_select" value="bed" /> - <param name="input" value="makeWindowBed1.bed" ftype="bed" /> - <param name="action_select" value="number" /> - <param name="number" value="15" /> + <param name="type|type_select" value="bed" /> + <param name="type|input" value="makeWindowBed1.bed" ftype="bed" /> + <param name="action|action_select" value="number" /> + <param name="action|number" value="15" /> <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> </test> </tests>
--- a/mergeBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/mergeBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>combine overlapping/nearby intervals into a single interval</description> <macros> <import>macros.xml</import> @@ -13,10 +13,13 @@ -d $distance $header @C_AND_O_ARGUMENT@ +#if $input.ext == "bam" + -bed +#end if > '${output}' ]]></command> <inputs> - <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> + <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Merge the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> <param name="strand" type="select" label="Calculation based on strandedness?"> <option value="" selected="true">Overlaps on either strand</option> <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option> @@ -25,7 +28,7 @@ </param> <param name="distance" argument="-d" type="integer" value="0" label="Maximum distance between features allowed for features to be merged" - help="That is, overlapping and/or book-ended features are merged"/> + help="Default 0: overlapping and/or book-ended features are merged. Note: negative values enforce the number of b.p. required for overlap."/> <expand macro="print_header" /> <expand macro="c_and_o_argument"> <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" /> @@ -38,20 +41,48 @@ <test> <param name="input" value="mergedBed1.bed" ftype="bed" /> <output name="output" file="mergedBed_result1.bed" ftype="bed" /> + <assert_command> + <not_has_text text="-s "/> + <not_has_text text="-S "/> + <has_text text="-d 0"/> + <not_has_text text="-c "/> + <not_has_text text="-o "/> + </assert_command> </test> <test> <param name="input" value="mergedBed2.bed" ftype="bed" /> <param name="strand" value="-s" /> <output name="output" file="mergedBed_result2.bed" ftype="bed" /> + <assert_command> + <has_text text="-s "/> + <not_has_text text="-S "/> + <has_text text="-d 0"/> + <not_has_text text="-c "/> + <not_has_text text="-o "/> + </assert_command> </test> <test> <param name="input" value="mergedBed3.bed" ftype="bed" /> <output name="output" file="mergedBed_result3.bed" ftype="bed" /> + <assert_command> + <not_has_text text="-s "/> + <not_has_text text="-S "/> + <has_text text="-d 0"/> + <not_has_text text="-c "/> + <not_has_text text="-o "/> + </assert_command> </test> <test> <param name="input" value="mergedBed4.bed" ftype="bed" /> <param name="distance" value="1000" /> <output name="output" file="mergedBed_result4.bed" ftype="bed" /> + <assert_command> + <not_has_text text="-s "/> + <not_has_text text="-S "/> + <has_text text="-d 1000"/> + <not_has_text text="-c "/> + <not_has_text text="-o "/> + </assert_command> </test> <test> <param name="input" value="mergedBed4.bed" ftype="bed" /> @@ -61,6 +92,13 @@ <param name="operation" value="count"/> </repeat> <output name="output" file="mergedBed_result5.bed" ftype="bed" /> + <assert_command> + <not_has_text text="-s "/> + <not_has_text text="-S "/> + <has_text text="-d 1000"/> + <has_text text="-c 1"/> + <has_text text="-o count"/> + </assert_command> </test> </tests> <help><![CDATA[
--- a/multiCov.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/multiCov.xml Fri Feb 21 21:38:34 2025 +0000 @@ -56,7 +56,7 @@ <param name="input" value="multiCov1.bed" ftype="bed" /> <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> <param name="q" value="1"/> - <param name="split" value=""/> + <param name="split" value="false"/> <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> </test> </tests>
--- a/multiIntersectBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/multiIntersectBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -69,24 +69,24 @@ </outputs> <tests> <test> - <param name="tag_select" value="tag" /> - <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> - <param name="empty_selector" value="" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> + <param name="empty|empty_selector" value="" /> <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" /> </test> <test> - <param name="tag_select" value="tag" /> - <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> - <param name="header" value="True" /> - <param name="empty_selector" value="" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> + <param name="header" value="true" /> + <param name="empty|empty_selector" value="" /> <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" /> </test> <test> - <param name="tag_select" value="tag" /> - <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" ftype="tabular" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> + <param name="empty|empty_selector" value="-empty" /> + <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="empty|genome_file_opts|genome" value="multiIntersectBed1.len" ftype="tabular" /> <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> </test> </tests>
--- a/randomBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/randomBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -11,8 +11,8 @@ @GENOME_FILE@ -l $length -n $intervals -#if str($seed.seed_choose) == "True": - -seed $seed.seed +#if str($seed) != "": + -seed $seed #end if > '$output' ]]></command> @@ -27,9 +27,8 @@ </outputs> <tests> <test> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="tabular" /> - <param name="seed_choose" value="False" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" /> <param name="length" value="5" /> <param name="intervals" value="3" /> <output name="output">
--- a/shuffleBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/shuffleBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -11,8 +11,8 @@ @GENOME_FILE@ -i '$inputA' $bedpe -#if str($seed.seed_choose) == "True": - -seed $seed.seed +#if str($seed) != "": + -seed $seed #end if #if str($add_bed.add_bed_select) == "not_be": -excl $add_bed.excl @@ -68,40 +68,36 @@ <tests> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="shuffleBed.len" ftype="tabular" /> - <param name="chrom" value="" /> - <param name="seed_choose" value="True" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" /> + <param name="chrom" value="false" /> <param name="seed" value="1" /> <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="shuffleBed.len" ftype="tabular" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" /> <param name="chrom" value="True" /> - <param name="seed_choose" value="True" /> <param name="seed" value="1" /> <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="shuffleBed.len" ftype="tabular" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" /> <conditional name="add_bed"> <param name="add_bed_select" value="not_be"/> <param name="excl" value="shuffleBed2.bed" ftype="bed" /> </conditional> - <param name="seed_choose" value="True" /> <param name="seed" value="1" /> <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="shuffleBed.len" ftype="bed" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="bed" /> <param name="allow_beyond" value="True" /> - <param name="seed_choose" value="True" /> <param name="seed" value="3" /> <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> </test>
--- a/slopBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/slopBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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> @@ -39,19 +39,19 @@ <tests> <test> <param name="inputA" value="a.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="bed" /> - <param name="addition_select" value="b" /> - <param name="b" value="5" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="bed" /> + <param name="addition|addition_select" value="b" /> + <param name="addition|b" value="5" /> <output name="output" file="slopBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="a.bed" ftype="bed" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9_chr1.len" ftype="bed" /> - <param name="addition_select" value="lr" /> - <param name="l" value="2" /> - <param name="r" value="3" /> + <param name="genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="bed" /> + <param name="addition|addition_select" value="lr" /> + <param name="addition|l" value="2" /> + <param name="addition|r" value="3" /> <output name="output" file="slopBed_result2.bed" ftype="bed" /> </test> </tests>
--- a/sortBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/sortBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jaccardBed_strand_result2.bed Fri Feb 21 21:38:34 2025 +0000 @@ -0,0 +1,2 @@ +intersection union jaccard n_intersections +0 0 -nan 0
--- a/unionBedGraphs.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/unionBedGraphs.xml Fri Feb 21 21:38:34 2025 +0000 @@ -66,43 +66,43 @@ </outputs> <tests> <test> - <param name="tag_select" value="tag" /> - <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> - <param name="empty_selector" value="" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="empty|empty_selector" value="" /> <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> </test> <test> - <param name="tag_select" value="tag" /> - <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> - <param name="header" value="True" /> - <param name="empty_selector" value="" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="header" value="true" /> + <param name="empty|empty_selector" value="" /> <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> </test> <test> - <param name="tag_select" value="tag" /> - <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" ftype="tabular" /> + <param name="tag|tag_select" value="tag" /> + <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="empty|empty_selector" value="-empty" /> + <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="empty|genome_file_opts|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="tag|tag_select" value="custom" /> + <repeat name="tag|bedgraphs"> <param name="input" value="unionBedGraphs1.bg" ftype="bedgraph" /> <param name="custom_name" value="first" /> </repeat> - <repeat name="bedgraphs"> + <repeat name="tag|bedgraphs"> <param name="input" value="unionBedGraphs2.bg" ftype="bedgraph" /> <param name="custom_name" value="second" /> </repeat> - <repeat name="bedgraphs"> + <repeat name="tag|bedgraphs"> <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" ftype="tabular" /> + <param name="empty|empty_selector" value="-empty" /> + <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" /> + <param name="empty|genome_file_opts|genome" value="unionBedGraphs1.len" ftype="tabular" /> <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> </test> </tests>
--- a/windowBed.xml Thu Mar 02 08:50:31 2023 +0000 +++ b/windowBed.xml Fri Feb 21 21:38:34 2025 +0000 @@ -77,16 +77,16 @@ <test> <param name="inputA" value="windowBedA.bed" ftype="bed" /> <param name="inputB" value="windowBedB.bed" ftype="bed" /> - <param name="addition_select" value="window" /> - <param name="w" value="5000" /> + <param name="addition|addition_select" value="window" /> + <param name="addition|w" value="5000" /> <output name="output" file="windowBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="windowBedA.bed" ftype="bed" /> <param name="inputB" value="windowBedB.bed" ftype="bed" /> - <param name="addition_select" value="lr" /> - <param name="l" value="200" /> - <param name="r" value="20000" /> + <param name="addition|addition_select" value="lr" /> + <param name="addition|l" value="200" /> + <param name="addition|r" value="20000" /> <output name="output" file="windowBed_result2.bed" ftype="bed" /> </test> </tests>