Mercurial > repos > iuc > bedtools
changeset 42:841fb4dc3ab3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 4046c1da68a09c7a3c275f6fe890ec71470fd74d"
| author | iuc |
|---|---|
| date | Wed, 12 Jan 2022 19:22:14 +0000 |
| parents | 7ab85ac5f64b |
| children | 07e8b80f278c |
| files | getfastaBed.xml test-data/getfastaBed_result3.bed test-data/getfastaBed_result4.bed test-data/nucBed2.bed |
| diffstat | 4 files changed, 27 insertions(+), 1 deletions(-) [+] |
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--- a/getfastaBed.xml Thu Nov 04 11:36:55 2021 +0000 +++ b/getfastaBed.xml Wed Jan 12 19:22:14 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@"> +<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>use intervals to extract sequences from a FASTA file</description> <macros> <import>macros.xml</import> @@ -16,6 +16,7 @@ ln -s '$fasta_file' 'input.fasta' && bedtools getfasta $name +$nameOnly $tab $strand $split @@ -40,6 +41,8 @@ </when> </conditional> <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false" + label="Use the 'name' column in the BED file and the coordinates for the FASTA headers in the output FASTA file" /> + <param argument="-nameOnly" type="boolean" truevalue="-nameOnly" falsevalue="" checked="false" label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" /> <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false" label="Report extract sequences in a tab-delimited format instead of in FASTA format" /> @@ -61,6 +64,7 @@ <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="False" /> <param name="split" value="False" /> + <param name="nameOnly" value="False" /> <output name="output" file="getfastaBed_result1.bed" ftype="fasta" /> </test> <test> @@ -68,8 +72,25 @@ <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="tab" value="True" /> <param name="split" value="False" /> + <param name="nameOnly" value="False" /> <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" /> </test> + <test> + <param name="input" value="nucBed1.bed" ftype="bed" /> + <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="tab" value="False" /> + <param name="split" value="False" /> + <param name="name" value="True" /> + <output name="output" file="getfastaBed_result3.bed" ftype="fasta" /> + </test> + <test> + <param name="input" value="nucBed2.bed" ftype="bed" /> + <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="tab" value="False" /> + <param name="split" value="False" /> + <param name="nameOnly" value="True" /> + <output name="output" file="getfastaBed_result4.bed" ftype="fasta" /> + </test> </tests> <help><![CDATA[ **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getfastaBed_result3.bed Wed Jan 12 19:22:14 2022 +0000 @@ -0,0 +1,2 @@ +>::chr1:10-100 +TTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGATAGAACTTCATGTGCCTGTA