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annotate macs2_bdgbroadcall.xml @ 17:424aefbd7777 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
author iuc
date Thu, 25 Apr 2019 17:49:05 -0400
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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 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="4.1.3">gawk</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12 @home_dir@
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13 macs2 bdgbroadcall
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14 --ifile '${ infile }'
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15 --cutoff-peak '${ cutoffpeak }'
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16 --cutoff-link '${ cutofflink }'
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17 --min-length '${ minlen }'
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18 --lvl1-max-gap '${ LVL1MAXGAP }'
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19 --lvl2-max-gap '${ LVL2MAXGAP }'
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20 --ofile "macs2_bdgbroadcall.bdg"
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21 &&
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22 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
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23 ]]></command>
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24 <inputs>
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25 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
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26 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
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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 (--cutoff)"/>
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28 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
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29 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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30 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
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31 help="It is recommended to set it as d value. Default=200 (--min-length)" />
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32 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
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33 help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
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34 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
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35 help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
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36 </inputs>
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37 <outputs>
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38 <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
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43 <param name="cutoffpeak" value="2.0"/>
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44 <param name="cutofflink" value="1.0"/>
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45 <param name="minlen" value="200"/>
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46 <param name="LVL1MAXGAP" value="30"/>
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47 <param name="LVL2MAXGAP" value="800"/>
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48 <output name="outfile" file="bdgbroadcall_output.bdg"/>
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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53
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54 This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.
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56 .. _MACS2: https://github.com/taoliu/MACS
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59 @citation@
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60 </help>
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61 <expand macro="citations" />
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62 </tool>