Mercurial > repos > iuc > bedtools
diff coverageBed.xml @ 46:64e2edfe7a2c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 23:28:38 +0000 |
| parents | a1a923cd89e8 |
| children |
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--- a/coverageBed.xml Thu Mar 02 08:52:08 2023 +0000 +++ b/coverageBed.xml Sat May 18 23:28:38 2024 +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="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[ @@ -155,5 +143,5 @@ @REFERENCES@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>