Mercurial > repos > iuc > bedtools

annotate getfastaBed.xml @ 26:c0fbce5dc84a 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 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children da6d7bc0a8b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
1 <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
17
a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 8
diff changeset
2 <description>use intervals to extract sequences from a FASTA file</description>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
3 <macros>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
5 </macros>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
6 <expand macro="requirements" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
7 <expand macro="stdio" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
8 <command>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
9 <![CDATA[
26
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
10 #if str( $fasta_source.fasta_source_selector ) == 'history':
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
11 #set $fasta_file = $fasta_source.fasta
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
12 #else
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
13 #set $fasta_file = $fasta_source.fasta_id.fields.path
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
14 #end if
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
15 bedtools getfasta
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
16 $name
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
17 $tab
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
18 $strand
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
19 $split
26
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
20 -fi '$fasta_file'
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
21 -bed '$input'
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
22 -fo '$output'
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
23 ]]>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
24 </command>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
25 <inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
26
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
27 <conditional name="fasta_source">
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
28 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
29 <option value="history" selected="True">History</option>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
30 <option value="preloaded">Server indexed files</option>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
31 </param>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
32 <when value="history">
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
33 <param name="fasta" format="fasta" type="data" label="Fasta file" />
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
34 </when>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
35 <when value="preloaded">
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
36 <param name="fasta_id" type="select">
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
37 <options from_data_table="all_fasta" />
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
38 </param>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
39 </when>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 17
diff changeset
40 </conditional>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
41 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
42 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
43 help="(-name)" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
44 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
45 label="Report extract sequences in a tab-delimited format instead of in FASTA format"
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
46 help="(-tab)" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
47 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
48 label="Force strandedness"
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
49 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
50 <expand macro="split" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
51 </inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
52 <outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
53 <data format="fasta" name="output">
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
54 <change_format>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
55 <when input="tab" value="-tab" format="tabular" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
56 </change_format>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
57 </data>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
58 </outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
59 <tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
60 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
61 <param name="input" value="nucBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
62 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
63 <param name="tab" value="False" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
64 <param name="split" value="False" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
65 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
66 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
67 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
68 <param name="input" value="nucBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
69 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
70 <param name="tab" value="True" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
71 <param name="split" value="False" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
72 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
73 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
74 </tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
75 <help>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
76 <![CDATA[
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
77 **What it does**
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
78
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
79 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
80
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
81 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
82
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
83 .. class:: warningmark
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
84
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
85 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
86
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
87 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
88
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
89 @REFERENCES@
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
90 ]]>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
91 </help>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
92 <expand macro="citations" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
93 </tool>