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1 <tool id="bedtools_fisher" name="FisherBed" 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 fisher
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11 $strand
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12 $split
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13 -a $inputA
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14 -b $inputB
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15 -f $overlap
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16 -g $genome
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17 $reciprocal
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18 $m
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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="inputA" type="data" label="BED/VCF/GFF file"/>
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24 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
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25 <expand macro="genome" />
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26 <expand macro="strand2" />
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27 <expand macro="split" />
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28 <expand macro="overlap" />
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29 <expand macro="reciprocal" />
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30 <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
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31 label="Merge overlapping intervals before looking at overlap" help="(-m)" />
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32 </inputs>
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33 <outputs>
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34 <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
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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="inputA" value="fisherBed1.bed" ftype="bed" />
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39 <param name="inputB" value="fisherBed2.bed" ftype="bed" />
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40 <param name="genome" value="fisherBed.len" ftype="tabular" />
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41 <output name="output" file="fisherBed_result1.bed" ftype="bed" />
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 **What it does**
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47
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48 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
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49
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50 @REFERENCES@
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51 ]]>
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52 </help>
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53 <expand macro="citations" />
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54 </tool>
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