Mercurial > repos > iuc > bedtools
annotate maskFastaBed.xml @ 26:c0fbce5dc84a draft
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 | ac2040a5e6ff |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>use intervals to mask sequences from a FASTA file</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools maskfasta | |
| 11 $soft | |
| 12 -mc "${mc}" | |
| 13 -fi "${fasta}" | |
| 14 -bed "${input}" | |
| 15 -fo "${output}" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> | |
| 20 <param format="fasta" name="fasta" type="data" label="Fasta file"/> | |
| 21 <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue="" | |
| 22 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" | |
| 23 help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" /> | |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
24 <param name="mc" type="text" value="N" |
| 8 | 25 label="Replace masking character" |
| 26 help="That is, instead of masking with Ns, use another character. (-mc)" /> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="fasta" name="output" /> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
| 34 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
| 35 <param name="soft" value="False" /> | |
| 36 <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" /> | |
| 37 </test> | |
| 38 <test> | |
| 39 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
| 40 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
| 41 <param name="soft" value="True" /> | |
| 42 <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 <![CDATA[ | |
| 47 **What it does** | |
| 48 | |
| 49 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. | |
| 50 | |
| 51 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png | |
| 52 | |
| 53 @REFERENCES@ | |
| 54 ]]> | |
| 55 </help> | |
| 56 <expand macro="citations" /> | |
| 57 </tool> |