Mercurial > repos > iuc > bedtools

comparison getfastaBed.xml @ 60:36d57dc82aa6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 4046c1da68a09c7a3c275f6fe890ec71470fd74d"
author iuc
date Wed, 12 Jan 2022 19:20:20 +0000
parents 539958feb49c
children 9f6bd4c9479f
comparison
equal deleted inserted replaced
59:539958feb49c 60:36d57dc82aa6
1 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>use intervals to extract sequences from a FASTA file</description> 2 <description>use intervals to extract sequences from a FASTA file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools" />
14 ln -s '${fasta_file}.fai' 'input.fasta.fai' && 14 ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
15 #end if 15 #end if
16 ln -s '$fasta_file' 'input.fasta' && 16 ln -s '$fasta_file' 'input.fasta' &&
17 bedtools getfasta 17 bedtools getfasta
18 $name 18 $name
19 $nameOnly
19 $tab 20 $tab
20 $strand 21 $strand
21 $split 22 $split
22 -fi 'input.fasta' 23 -fi 'input.fasta'
23 -bed '$input' 24 -bed '$input'
38 <options from_data_table="fasta_indexes" /> 39 <options from_data_table="fasta_indexes" />
39 </param> 40 </param>
40 </when> 41 </when>
41 </conditional> 42 </conditional>
42 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false" 43 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
44 label="Use the 'name' column in the BED file and the coordinates for the FASTA headers in the output FASTA file" />
45 <param argument="-nameOnly" type="boolean" truevalue="-nameOnly" falsevalue="" checked="false"
43 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" /> 46 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
44 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false" 47 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
45 label="Report extract sequences in a tab-delimited format instead of in FASTA format" /> 48 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
46 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" 49 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
47 label="Force strandedness" 50 label="Force strandedness"
59 <test> 62 <test>
60 <param name="input" value="nucBed1.bed" ftype="bed" /> 63 <param name="input" value="nucBed1.bed" ftype="bed" />
61 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 64 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
62 <param name="tab" value="False" /> 65 <param name="tab" value="False" />
63 <param name="split" value="False" /> 66 <param name="split" value="False" />
67 <param name="nameOnly" value="False" />
64 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" /> 68 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
65 </test> 69 </test>
66 <test> 70 <test>
67 <param name="input" value="nucBed1.bed" ftype="bed" /> 71 <param name="input" value="nucBed1.bed" ftype="bed" />
68 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 72 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
69 <param name="tab" value="True" /> 73 <param name="tab" value="True" />
70 <param name="split" value="False" /> 74 <param name="split" value="False" />
75 <param name="nameOnly" value="False" />
71 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" /> 76 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
77 </test>
78 <test>
79 <param name="input" value="nucBed1.bed" ftype="bed" />
80 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
81 <param name="tab" value="False" />
82 <param name="split" value="False" />
83 <param name="name" value="True" />
84 <output name="output" file="getfastaBed_result3.bed" ftype="fasta" />
85 </test>
86 <test>
87 <param name="input" value="nucBed2.bed" ftype="bed" />
88 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
89 <param name="tab" value="False" />
90 <param name="split" value="False" />
91 <param name="nameOnly" value="True" />
92 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
72 </test> 93 </test>
73 </tests> 94 </tests>
74 <help><![CDATA[ 95 <help><![CDATA[
75 **What it does** 96 **What it does**
76 97