Mercurial > repos > iuc > bedtools
annotate maskFastaBed.xml @ 40:58451dcd076d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f
| author | iuc |
|---|---|
| date | Sun, 18 Feb 2018 15:06:49 -0500 |
| parents | ac2040a5e6ff |
| children | d279800f4ff9 |
| 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
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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 $soft | |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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12 -mc '${mc}' |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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13 -fi '${fasta}' |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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14 -bed '${input}' |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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15 -fo '${output}' |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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16 $fullheader |
| 8 | 17 ]]> |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> | |
| 21 <param format="fasta" name="fasta" type="data" label="Fasta file"/> | |
| 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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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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25 <param name="mc" type="text" value="N" |
| 8 | 26 label="Replace masking character" |
| 27 help="That is, instead of masking with Ns, use another character. (-mc)" /> | |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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28 <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue="" |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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29 label="Use full fasta header." |
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
26
diff
changeset
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30 help="By default, only the word before the first space or tab is used"/> |
| 8 | 31 </inputs> |
| 32 <outputs> | |
| 33 <data format="fasta" name="output" /> | |
| 34 </outputs> | |
| 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> | |
| 49 <help> | |
| 50 <![CDATA[ | |
| 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@ | |
| 58 ]]> | |
| 59 </help> | |
| 60 <expand macro="citations" /> | |
| 61 </tool> |