| Previous changeset 43:07e8b80f278c (2022-04-01) Next changeset 45:a1a923cd89e8 (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 03a91f6c42c75dc36d09505c2e6a2236178e4695 |
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modified:
mergeBed.xml sortBed.xml test-data/mergedBed_result2.bed test-data/sortBed_result2.bed |
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| diff -r 07e8b80f278c -r 589e7e57fd6d mergeBed.xml --- a/mergeBed.xml Fri Apr 01 19:02:51 2022 +0000 +++ b/mergeBed.xml Mon Feb 20 21:49:48 2023 +0000 |
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| @@ -41,12 +41,11 @@ </test> <test> <param name="input" value="mergedBed2.bed" ftype="bed" /> - <param name="strandedness" value="-s" /> + <param name="strand" value="-s" /> <output name="output" file="mergedBed_result2.bed" ftype="bed" /> </test> <test> <param name="input" value="mergedBed3.bed" ftype="bed" /> - <param name="report_number" value="-n" /> <output name="output" file="mergedBed_result3.bed" ftype="bed" /> </test> <test> |
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| diff -r 07e8b80f278c -r 589e7e57fd6d sortBed.xml --- a/sortBed.xml Fri Apr 01 19:02:51 2022 +0000 +++ b/sortBed.xml Mon Feb 20 21:49:48 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>order the intervals</description> <macros> <import>macros.xml</import> @@ -25,7 +25,7 @@ <option value="-chrThenScoreA">chromosome, then by score (asc).</option> <option value="-chrThenScoreD">chromosome, then by score (desc).</option> </param> - <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" /> + <expand macro="input_conditional_genome_file" optional="true" help="Sort according to the chromosomes declared in a genome file" /> </inputs> <outputs> <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/> |
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| diff -r 07e8b80f278c -r 589e7e57fd6d test-data/mergedBed_result2.bed --- a/test-data/mergedBed_result2.bed Fri Apr 01 19:02:51 2022 +0000 +++ b/test-data/mergedBed_result2.bed Mon Feb 20 21:49:48 2023 +0000 |
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| @@ -1,2 +1,3 @@ -chr1 100 500 +chr1 100 250 +chr1 250 500 chr1 501 1000 |
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| diff -r 07e8b80f278c -r 589e7e57fd6d test-data/sortBed_result2.bed --- a/test-data/sortBed_result2.bed Fri Apr 01 19:02:51 2022 +0000 +++ b/test-data/sortBed_result2.bed Mon Feb 20 21:49:48 2023 +0000 |
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| @@ -1,3 +1,3 @@ chr1 800 1000 +chr10 80 180 chr2 1 10 -chr10 80 180 |