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1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 bedtools nuc
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11 $strand
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12 $seq
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13 $pattern
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14 $case
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15 -fi $fasta
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16 -bed $input
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17 > $output
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
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22 <param format="fasta" name="fasta" type="data" label="FASTA file"/>
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23
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24 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
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25 label="Profile the sequence according to strand" help="(-s)"/>
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26 <param name="seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
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27 label="Print the extracted sequence" help="(-seq)"/>
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28 <param name="pattern" type="boolean" checked="false" truevalue="-pattern" falsevalue=""
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29 label="Report the number of times a user-defined sequence is observed" help="case-sensitive (-pattern)" />
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30 <param name="case" type="boolean" checked="false" truevalue="-C" falsevalue=""
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31 label="Igore case when matching -pattern" help="(-C)"/>
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32 </inputs>
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33 <outputs>
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34 <data format="tabular" name="output" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="nucBed1.bed" ftype="bed" />
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39 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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40 <output name="output" file="nucBed_result1.bed" ftype="tabular" />
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41 </test>
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42 <test>
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43 <param name="input" value="nucBed1.bed" ftype="bed" />
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44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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45 <param name="seq" value="True" />
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46 <output name="output" file="nucBed_result2.bed" ftype="tabular" />
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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51 **What it does**
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52
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53 Profiles the nucleotide content of intervals in a fasta file.
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54
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55 @REFERENCES@
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56 ]]>
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57 </help>
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58 <expand macro="citations" />
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59 </tool>
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