Mercurial > repos > iuc > bedtools
comparison maskFastaBed.xml @ 1:82aac94b06c3 draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 08 Jan 2015 14:25:51 -0500 |
| parents | b8348686a0b9 |
| children | 607c0576c6ab |
comparison
equal
deleted
inserted
replaced
| 0:b8348686a0b9 | 1:82aac94b06c3 |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command> | 8 <command> |
| 9 <![CDATA[ | |
| 9 bedtools maskfasta | 10 bedtools maskfasta |
| 10 $soft | 11 $soft |
| 11 -mc $mc | 12 -mc "${mc}" |
| 12 -fi $fasta | 13 -fi "${fasta}" |
| 13 -bed $inputA | 14 -bed "${input}" |
| 14 -fo $output | 15 -fo "${output}" |
| 16 ]]> | |
| 15 </command> | 17 </command> |
| 16 <inputs> | 18 <inputs> |
| 17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | 19 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> |
| 18 <param format="fasta" name="fasta" type="data" label="Fasta file"/> | 20 <param format="fasta" name="fasta" type="data" label="Fasta file"/> |
| 19 | 21 <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue="" |
| 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" /> | 22 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" |
| 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." /> | 23 help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" /> |
| 24 <param name="mc" type="text" value="N" length="1" | |
| 25 label="Replace masking character" | |
| 26 help="That is, instead of masking with Ns, use another character. (-mc)" /> | |
| 22 </inputs> | 27 </inputs> |
| 23 <outputs> | 28 <outputs> |
| 24 <data format="fasta" name="output" /> | 29 <data format="fasta" name="output" /> |
| 25 </outputs> | 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> | |
| 26 <help> | 45 <help> |
| 27 | 46 <![CDATA[ |
| 28 **What it does** | 47 **What it does** |
| 29 | 48 |
| 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. | 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. |
| 31 | 50 |
| 32 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png | 51 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png |
| 33 | 52 |
| 34 @REFERENCES@ | 53 @REFERENCES@ |
| 54 ]]> | |
| 35 </help> | 55 </help> |
| 36 <expand macro="citations" /> | 56 <expand macro="citations" /> |
| 37 </tool> | 57 </tool> |