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1 <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
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2 <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>macs2_macros.xml</import>
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7 </macros>
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8 <command>
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9 macs2 refinepeak
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10 -b "${ bed_infile }"
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11 -i "${ infile }"
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12 --format '${ infile.extension.upper() }'
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13 --cutoff "${ cutoff }"
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14 --window-size "${ winsize }"
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15 --ofile "${ outfile }"
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16 </command>
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17 <expand macro="stdio" />
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18 <inputs>
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19 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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20 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
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21 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
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22 <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />
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23 </inputs>
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24
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25 <outputs>
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26 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="infile" value="ChIP_200K.bed" ftype="bed"/>
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31 <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/>
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32 <param name="cutoff" value="5.0"/>
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33 <param name="winsize" value="200"/>
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34 <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/>
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35 </test>
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36 </tests>
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37 <help>
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38 **What it does**
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39
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40 (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.
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41
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42 @citation@
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43 </help>
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44 <expand macro="citations" />
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45 </tool>
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