Mercurial > repos > iuc > bedtools
annotate nucBed.xml @ 11:7308cc546a36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:35 -0400 |
| parents | 607c0576c6ab |
| children | b3c147390100 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0"> |
|
4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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2 <description>profile the nucleotide content of intervals in 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 nuc |
| 11 $strand | |
| 12 $seq | |
| 13 $pattern | |
| 14 $case | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
15 -fi '$fasta' |
|
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
16 -bed '$input' |
|
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
17 > '$output' |
| 1 | 18 ]]> |
| 0 | 19 </command> |
| 20 <inputs> | |
| 1 | 21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> |
| 22 <param format="fasta" name="fasta" type="data" label="FASTA file"/> | |
| 0 | 23 |
| 1 | 24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 25 label="Profile the sequence according to strand" help="(-s)"/> | |
| 26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" | |
| 27 label="Print the extracted sequence" help="(-seq)"/> | |
| 28 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" | |
| 29 label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" /> | |
| 30 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" | |
| 31 label="Igore case when matching -pattern" help="(-C)"/> | |
| 0 | 32 </inputs> |
| 33 <outputs> | |
| 1 | 34 <data format="tabular" name="output" /> |
| 0 | 35 </outputs> |
| 1 | 36 <tests> |
| 37 <test> | |
| 38 <param name="input" value="nucBed1.bed" ftype="bed" /> | |
| 39 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> | |
| 40 <output name="output" file="nucBed_result1.bed" ftype="tabular" /> | |
| 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="seq" value="True" /> | |
| 46 <output name="output" file="nucBed_result2.bed" ftype="tabular" /> | |
| 47 </test> | |
| 48 </tests> | |
| 0 | 49 <help> |
| 1 | 50 <![CDATA[ |
| 0 | 51 **What it does** |
| 52 | |
| 53 Profiles the nucleotide content of intervals in a fasta file. | |
| 54 | |
| 55 @REFERENCES@ | |
| 1 | 56 ]]> |
| 0 | 57 </help> |
| 58 <expand macro="citations" /> | |
| 59 </tool> |