Mercurial > repos > iuc > bedtools
annotate getfastaBed.xml @ 12:7b3aaff0d78c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
author | iuc |
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date | Fri, 28 Oct 2016 12:54:40 -0400 |
parents | 7308cc546a36 |
children | 13400f3c3ec5 |
rev | line source |
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0 | 1 <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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2 <description>use intervals to extract sequences from a FASTA file</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
8 <command> | |
1 | 9 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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10 #if str( $fasta_source.fasta_source_selector ) == 'history': |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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11 #set $fasta_file = $fasta_source.fasta |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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12 #else |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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13 #set $fasta_file = $fasta_source.fasta_id.fields.path |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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14 #end if |
0 | 15 bedtools getfasta |
16 $name | |
17 $tab | |
18 $strand | |
19 $split | |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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20 -fi '$fasta_file' |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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21 -bed '$input' |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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22 -fo '$output' |
1 | 23 ]]> |
0 | 24 </command> |
25 <inputs> | |
1 | 26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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27 <conditional name="fasta_source"> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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28 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file"> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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29 <option value="history" selected="True">History</option> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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30 <option value="preloaded">Server indexed files</option> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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31 </param> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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32 <when value="history"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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33 <param name="fasta" format="fasta" type="data" label="Fasta file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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34 </when> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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35 <when value="preloaded"> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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36 <param name="fasta_id" type="select"> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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37 <options from_data_table="all_fasta" /> |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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38 </param> |
10
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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39 </when> |
c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
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40 </conditional> |
1 | 41 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" |
42 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" | |
43 help="(-name)" /> | |
44 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" | |
45 label="Report extract sequences in a tab-delimited format instead of in FASTA format" | |
46 help="(-tab)" /> | |
47 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" | |
48 label="Force strandedness" | |
49 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" /> | |
50 <expand macro="split" /> | |
0 | 51 </inputs> |
52 <outputs> | |
1 | 53 <data format="fasta" name="output"> |
54 <change_format> | |
55 <when input="tab" value="-tab" format="tabular" /> | |
56 </change_format> | |
57 </data> | |
0 | 58 </outputs> |
1 | 59 <tests> |
60 <test> | |
61 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
62 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
63 <param name="tab" value="False" /> | |
64 <param name="split" value="False" /> | |
65 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" /> | |
66 </test> | |
67 <test> | |
68 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
69 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
70 <param name="tab" value="True" /> | |
71 <param name="split" value="False" /> | |
72 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" /> | |
73 </test> | |
74 </tests> | |
0 | 75 <help> |
1 | 76 <![CDATA[ |
0 | 77 **What it does** |
78 | |
1 | 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>:<start>-<end>”. |
0 | 80 |
81 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png | |
82 | |
83 .. class:: warningmark | |
84 | |
85 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. | |
86 | |
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. | |
88 | |
89 @REFERENCES@ | |
1 | 90 ]]> |
0 | 91 </help> |
92 <expand macro="citations" /> | |
93 </tool> |