Mercurial > repos > iuc > bedtools

annotate nucBed.xml @ 42:841fb4dc3ab3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 4046c1da68a09c7a3c275f6fe890ec71470fd74d"
author iuc
date Wed, 12 Jan 2022 19:22:14 +0000
parents 7ab85ac5f64b
children
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>profile the nucleotide content of intervals in a FASTA file</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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 ln -s '$fasta' 'input.fasta' &&
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11 bedtools nuc
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12 $s
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13 $seq
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14 #if str($pattern):
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15 -pattern '$pattern'
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16 $C
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17 #end if
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18 -fi 'input.fasta'
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19 -bed '$input'
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20 > '$output'
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21 ]]></command>
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22 <inputs>
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23 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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24 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
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25
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26 <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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27 label="Profile the sequence according to strand" />
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28 <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
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29 label="Print the extracted sequence" />
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30 <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
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31 <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
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32 </param>
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33 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false"
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34 label="Ignore case when matching -pattern"/>
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="tabular" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="nucBed1.bed" ftype="bed" />
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42 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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43 <output name="output" file="nucBed_result1.bed" ftype="tabular" />
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44 </test>
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45 <test>
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46 <param name="input" value="nucBed1.bed" ftype="bed" />
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47 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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48 <param name="seq" value="True" />
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49 <output name="output" file="nucBed_result2.bed" ftype="tabular" />
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50 </test>
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51 <test>
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52 <param name="input" value="nucBed1.bed" ftype="bed" />
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53 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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54 <param name="seq" value="True" />
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55 <param name="pattern" value="TAC" />
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56 <output name="output" file="nucBed_result3.bed" ftype="tabular" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 **What it does**
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61
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62 Profiles the nucleotide content of intervals in a fasta file.
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63
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64 @REFERENCES@
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65 ]]></help>
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66 <expand macro="citations" />
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67 </tool>