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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96
author iuc
date Mon, 16 Oct 2023 13:18:37 +0000
parents 640d3af5d833
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640d3af5d833 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
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1 <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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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 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 @home_dir@
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12 macs2 refinepeak
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13 -b '${ bed_infile }'
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14 -i '${ infile }'
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15 --format '${ infile.extension.upper() }'
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16 --cutoff '${ cutoff }'
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17 --window-size '${ winsize }'
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18 --ofile '${ outfile }'
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19 @buffer_size@
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20 ]]></command>
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21 <inputs>
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22 <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
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23 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
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24 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
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25 <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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26 <expand macro="buffer_size"/>
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27 </inputs>
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28
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29 <outputs>
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30 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="infile" value="refinepeak_bam_input.bam" ftype="bam"/>
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35 <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/>
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36 <param name="cutoff" value="5.0"/>
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37 <param name="winsize" value="200"/>
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38 <output name="outfile" file="refinepeak_output.bed"/>
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39 </test>
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40 </tests>
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41 <help>
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42 <![CDATA[
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43 **What it does**
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44
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45 This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline.
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47 .. _MACS2: https://github.com/taoliu/MACS
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48 .. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/
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50 @citation@
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51 ]]>
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52 </help>
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53 <expand macro="citations" />
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54 </tool>