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1 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
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2 <description>Call broad 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 bdgbroadcall
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12 --ifile "${ infile }"
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13 --cutoff-peak "${ cutoffpeak }"
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14 --cutoff-link "${ cutofflink }"
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15 --min-length "${ minlen }"
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16 --lvl1-max-gap "${ LVL1MAXGAP }"
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17 --lvl2-max-gap "${ LVL2MAXGAP }"
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18 --ofile "macs2_bdgbroadcall.bdg"
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19 &&
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20 awk '!/^track name/' "macs2_bdgbroadcall.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 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
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26 help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/>
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27 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
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28 help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. default: 1 (--cutoff-link)"/>
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29 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
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30 help="It is recommended to set it as d value." />
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31 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
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32 help="It is recommended to set it to tag size" />
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33 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
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34 help="It is recommended to set it to 4 times of d value" />
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35 </inputs>
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36 <outputs>
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37 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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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="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" />
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42 <param name="cutoffpeak" value="2.0"/>
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43 <param name="cutofflink" value="1.0"/>
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44 <param name="minlen" value="200"/>
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45 <param name="LVL1MAXGAP" value="30"/>
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46 <param name="LVL2MAXGAP" value="800"/>
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47 <output name="outfile" file="bdgbroadcall_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 broad peaks from bedGraph output.
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54 bdgbroadcall from macs2
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55
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56 @citation@
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57 </help>
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58 <expand macro="citations" />
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59 </tool>
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