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1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="2.0.10.0">
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2 <description>Call peaks from bedGraph output</description>
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3 <expand macro="requirements">
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4 <requirement type="package" version="4.1.0">gnu_awk</requirement>
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5 </expand>
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6 <expand macro="version_command" />
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7 <macros>
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8 <import>macs2_macros.xml</import>
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9 </macros>
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10 <command>
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11 macs2 bdgpeakcall
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12 --ifile "${ infile }"
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13 --cutoff "${ cutoff }"
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14 --min-length "${ minlen }"
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15 --max-gap "${ maxgap }"
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16 ${ callsummits }
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17 ${ notrackline }
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18 --ofile "macs2_bdgpeakcall.bdg"
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19 &&
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20 awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
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21 </command>
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22 <expand macro="stdio" />
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23 <inputs>
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24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
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25
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26 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
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27 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5.0 (--cutoff)"/>
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28 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/>
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29 <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/>
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30
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31 <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
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32 label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region."
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33 help="(-call-summits)"/>
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34 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False"
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35 label="Include trackline into bedGraph output"
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36 help="required by USCS (--no-trackline)"/>
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37 </inputs>
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38 <outputs>
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39 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" />
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44 <param name="cutoff" value="5.0"/>
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45 <param name="minlen" value="200"/>
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46 <param name="maxgap" value="30"/>
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47 <output name="outfile" file="bdgpeakcall_on_callpeak_treatment.tabular"/>
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48 </test>
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49 </tests>
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50 <help>
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51 **What it does**
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52
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53 Call peaks from bedGraph output.
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54 bdgpeakcall from macs2
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55
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56
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57 @citation@
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58 </help>
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59 </tool>
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