| Previous changeset 17:44867b59dbf2 (2017-09-05) Next changeset 19:a8eabd2838f6 (2017-12-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit dc0d10f28180ec2b2d1b0beac637601ea859e8f2 |
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modified:
coverageBed.xml |
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added:
test-data/coverageBed_result2_F1.bed test-data/coverageBed_result3_f1r.bed |
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| diff -r 44867b59dbf2 -r 18aeac3cd1db coverageBed.xml --- a/coverageBed.xml Tue Sep 05 15:40:14 2017 -0400 +++ b/coverageBed.xml Sat Oct 21 07:57:53 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1"> <description>of features in file B on the features in file A (bedtools coverage)</description> <macros> <import>macros.xml</import> @@ -14,6 +14,14 @@ $hist $split $strandedness + #if str($overlap_a) != "None" and str($overlap_a): + -f '$overlap_a' + #end if + #if str($overlap_b) != "None" and str($overlap_b): + -F '$overlap_b' + #end if + $reciprocal_overlap + $a_or_b -a '$inputA' -b '$inputBs' | sort -k1,1 -k2,2n @@ -32,6 +40,26 @@ <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" 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 (-hist)" /> + <param name="overlap_a" type="text" + label="Minimum overlap required as a fraction of A." + help="Default is 1E-9 (i.e., 1bp). (-f)"> + <sanitizer invalid_char=""> + <valid initial="string.digits"><add value=",."/></valid> + </sanitizer> + </param> + <param name="overlap_b" type="text" + label="Minimum overlap required as a fraction of B." + help="Default is 1E-9 (i.e., 1bp). (-F)"> + <sanitizer invalid_char=""> + <valid initial="string.digits"><add value=",."/></valid> + </sanitizer> + </param> + <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue="" + 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 (-r)" /> + <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue="" + 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. (-e)" /> </inputs> <outputs> <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> @@ -39,9 +67,22 @@ <tests> <test> <param name="inputA" value="coverageBedA.bed" ftype="bed" /> - <param name="genome" value="coverageBedB.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="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="1" /> + <param name="reciprocal_overlap" value="true" /> + <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r 44867b59dbf2 -r 18aeac3cd1db test-data/coverageBed_result2_F1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverageBed_result2_F1.bed Sat Oct 21 07:57:53 2017 -0400 |
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| @@ -0,0 +1,4 @@ +chr1 10 20 0 0 10 0.0000000 +chr1 20 30 0 0 10 0.0000000 +chr1 30 40 0 0 10 0.0000000 +chr1 100 200 1 100 100 1.0000000 |
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| diff -r 44867b59dbf2 -r 18aeac3cd1db test-data/coverageBed_result3_f1r.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverageBed_result3_f1r.bed Sat Oct 21 07:57:53 2017 -0400 |
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| @@ -0,0 +1,4 @@ +chr1 10 20 0 0 10 0.0000000 +chr1 20 30 0 0 10 0.0000000 +chr1 30 40 0 0 10 0.0000000 +chr1 100 200 1 100 100 1.0000000 |