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comparison maskFastaBed.xml @ 0:b8348686a0b9 draft

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Imported from capsule None
author iuc
date Tue, 04 Nov 2014 01:45:04 -0500
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children 82aac94b06c3
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1 <tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 bedtools maskfasta
10 $soft
11 -mc $mc
12 -fi $fasta
13 -bed $inputA
14 -fo $output
15 </command>
16 <inputs>
17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
18 <param format="fasta" name="fasta" type="data" label="Fasta file"/>
19
20 <param name="soft" type="boolean" checked="false" truevalue="-name" falsevalue="" label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence. By default, hard-masking (that is, conversion to Ns) is performed" />
21 <param name="mc" type="text" value="N" length="1" falsevalue="" label="Replace masking character. That is, instead of masking with Ns, use another character." />
22 </inputs>
23 <outputs>
24 <data format="fasta" name="output" />
25 </outputs>
26 <help>
27
28 **What it does**
29
30 bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.
31
32 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png
33
34 @REFERENCES@
35 </help>
36 <expand macro="citations" />
37 </tool>