Mercurial > repos > iuc > bedtools
changeset 29:6bb3cd018203 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b
| author | iuc |
|---|---|
| date | Tue, 24 Jul 2018 11:49:55 -0400 |
| parents | 6283d16e40ed |
| children | db1841942d2b |
| files | coverageBed.xml test-data/multicov1_by_srma_in3.cov.bed |
| diffstat | 2 files changed, 15 insertions(+), 2 deletions(-) [+] |
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--- a/coverageBed.xml Sun Jun 24 11:52:38 2018 -0400 +++ b/coverageBed.xml Tue Jul 24 11:49:55 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2"> +<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.3"> <description>of features in file B on the features in file A (bedtools coverage)</description> <macros> <import>macros.xml</import> @@ -26,7 +26,7 @@ #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': -b '$reduce_or_iterate.inputB' #if $reduce_or_iterate.inputB.is_of_type('bam'): - -sorted -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5) + -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' | sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5) #end if #else: #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB]) @@ -96,6 +96,17 @@ <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" /> + <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" /> + <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" />