Mercurial > repos > iuc > bedtools
annotate maskFastaBed.xml @ 19:a8eabd2838f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
| author | iuc |
|---|---|
| date | Fri, 08 Dec 2017 03:26:42 -0500 |
| parents | c78cf6fe3018 |
| children | 95a3b2c25bd1 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
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changeset
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2 <description>use intervals to mask 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[ |
| 0 | 10 bedtools maskfasta |
| 1 | 11 $soft |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
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12 -mc '${mc}' |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
13 -fi '${fasta}' |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
14 -bed '${input}' |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
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15 -fo '${output}' |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
16 $fullheader |
| 1 | 17 ]]> |
| 0 | 18 </command> |
| 19 <inputs> | |
| 1 | 20 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> |
| 0 | 21 <param format="fasta" name="fasta" type="data" label="Fasta file"/> |
| 1 | 22 <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue="" |
| 23 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" | |
| 24 help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" /> | |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
4
diff
changeset
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25 <param name="mc" type="text" value="N" |
| 1 | 26 label="Replace masking character" |
| 27 help="That is, instead of masking with Ns, use another character. (-mc)" /> | |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
28 <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue="" |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
29 label="Use full fasta header." |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
|
30 help="By default, only the word before the first space or tab is used"/> |
| 0 | 31 </inputs> |
| 32 <outputs> | |
| 33 <data format="fasta" name="output" /> | |
| 34 </outputs> | |
| 1 | 35 <tests> |
| 36 <test> | |
| 37 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
| 38 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
| 39 <param name="soft" value="False" /> | |
| 40 <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" /> | |
| 41 </test> | |
| 42 <test> | |
| 43 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
| 44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
| 45 <param name="soft" value="True" /> | |
| 46 <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" /> | |
| 47 </test> | |
| 48 </tests> | |
| 0 | 49 <help> |
| 1 | 50 <![CDATA[ |
| 0 | 51 **What it does** |
| 52 | |
| 53 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. | |
| 54 | |
| 55 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png | |
| 56 | |
| 57 @REFERENCES@ | |
| 1 | 58 ]]> |
| 0 | 59 </help> |
| 60 <expand macro="citations" /> | |
| 61 </tool> |