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annotate fisherBed.xml @ 40:a68aa6c1204a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
author iuc
date Thu, 09 Sep 2021 13:04:07 +0000
parents 3e38c9b3214f
children 7ab85ac5f64b
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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_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>calculate Fisher statistic between two feature files</description>
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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 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 @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 ]]></command>
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21 <inputs>
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22 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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23 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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24 <expand macro="input_conditional_genome_file" />
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25 <expand macro="strand2" />
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26 <expand macro="split" />
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27 <expand macro="overlap" />
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28 <expand macro="reciprocal" />
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29 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false"
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30 label="Merge overlapping intervals before looking at overlap" />
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31 </inputs>
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32 <outputs>
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33 <data name="output" format_source="inputA" metadata_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="inputA" value="fisherBed1.bed" ftype="bed" />
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38 <param name="inputB" value="fisherBed2.bed" ftype="bed" />
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39 <param name="genome_file_opts_selector" value="hist" />
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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><![CDATA[
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45 **What it does**
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46
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47 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
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48
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49 @REFERENCES@
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>