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annotate fisherBed.xml @ 31:e19bebe96cd2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184
author iuc
date Tue, 20 Nov 2018 10:34:42 -0500
parents 95a3b2c25bd1
children 4f7a5ccd2ae9
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1 <tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
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2 <description>calculate Fisher statistic between two feature files</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_FILE@
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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="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
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24 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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25 <expand macro="input_conditional_genome_file" />
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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_file_opts_selector" value="hist" />
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41 <param name="genome" value="fisherBed.len" ftype="tabular" />
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42 <output name="output" file="fisherBed_result1.bed" ftype="bed" />
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43 </test>
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44 </tests>
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45 <help>
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46 <![CDATA[
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47 **What it does**
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48
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49 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
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50
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51 @REFERENCES@
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52 ]]>
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53 </help>
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54 <expand macro="citations" />
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55 </tool>