Mercurial > repos > iuc > bedtools
annotate maskFastaBed.xml @ 30:db1841942d2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3
| author | iuc |
|---|---|
| date | Fri, 17 Aug 2018 05:42:39 -0400 |
| parents | 95a3b2c25bd1 |
| children | 4f7a5ccd2ae9 |
| 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
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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
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13 -fi '${fasta}' |
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a8eabd2838f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
10
diff
changeset
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14 -bed '${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
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16 $fullheader |
| 1 | 17 ]]> |
| 0 | 18 </command> |
| 19 <inputs> | |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
19
diff
changeset
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20 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ 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
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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
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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> |