Mercurial > repos > iuc > bedtools
comparison nucBed.xml @ 1:82aac94b06c3 draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 08 Jan 2015 14:25:51 -0500 |
| parents | b8348686a0b9 |
| children | 607c0576c6ab |
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| 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 nuc | 10 bedtools nuc |
| 10 $strand | 11 $strand |
| 11 $seq | 12 $seq |
| 12 $pattern | 13 $pattern |
| 13 $case | 14 $case |
| 14 -fi $fasta | 15 -fi $fasta |
| 15 -bed $inputA | 16 -bed $input |
| 16 > $output | 17 > $output |
| 18 ]]> | |
| 17 </command> | 19 </command> |
| 18 <inputs> | 20 <inputs> |
| 19 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | 21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> |
| 20 <param format="fasta" name="fasta" type="data" label="Fasta file"/> | 22 <param format="fasta" name="fasta" type="data" label="FASTA file"/> |
| 21 | 23 |
| 22 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Profile the sequence according to strand." /> | 24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 23 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" label="Print the extracted sequence." /> | 25 label="Profile the sequence according to strand" help="(-s)"/> |
| 24 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue="" label="Report the number of times a user-defined sequence is observed (case-sensitive)." /> | 26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" |
| 25 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Igore case when matching -pattern." /> | 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)"/> | |
| 26 </inputs> | 32 </inputs> |
| 27 <outputs> | 33 <outputs> |
| 28 <data format="fasta" name="output" /> | 34 <data format="tabular" name="output" /> |
| 29 </outputs> | 35 </outputs> |
| 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> | |
| 30 <help> | 49 <help> |
| 31 | 50 <![CDATA[ |
| 32 **What it does** | 51 **What it does** |
| 33 | 52 |
| 34 Profiles the nucleotide content of intervals in a fasta file. | 53 Profiles the nucleotide content of intervals in a fasta file. |
| 35 | 54 |
| 36 @REFERENCES@ | 55 @REFERENCES@ |
| 56 ]]> | |
| 37 </help> | 57 </help> |
| 38 <expand macro="citations" /> | 58 <expand macro="citations" /> |
| 39 </tool> | 59 </tool> |