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annotate nucBed.xml @ 38:3f852f713d24 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
author iuc
date Sun, 21 Jan 2018 07:16:59 -0500
parents 7f4f9bb165c9
children d279800f4ff9
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3f852f713d24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
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1 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.1">
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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="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 $s
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12 $seq
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13 #if str($pattern):
3f852f713d24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
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14 -pattern '$pattern'
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15 $C
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16 #end if
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17 -fi '$fasta'
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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18 -bed '$input'
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19 > '$output'
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
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24 <param format="fasta" name="fasta" type="data" label="FASTA file"/>
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25
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26 <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
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27 label="Profile the sequence according to strand" />
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28 <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue=""
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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" checked="false" truevalue="-C" falsevalue=""
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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 format="tabular" name="output" />
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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" />
3f852f713d24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
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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" />
3f852f713d24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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61 **What it does**
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63 Profiles the nucleotide content of intervals in a fasta file.
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65 @REFERENCES@
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66 ]]>
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67 </help>
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68 <expand macro="citations" />
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69 </tool>