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annotate macs2_bdgpeakcall.xml @ 11:cb785e26207c draft

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author iuc
date Tue, 06 Mar 2018 07:25:31 -0500
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children 640d3af5d833
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1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
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2 <description>Call 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 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 @home_dir@
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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 ${ cutoff_analysis }
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17 ${ notrackline }
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18 --ofile '${ outfile }'
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19 ]]></command>
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20 <inputs>
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21 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
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22 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
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23 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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24 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>
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25 <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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26 <param name="cutoff_analysis" type="boolean" truevalue="--cutoff-analysis" falsevalue="" checked="False" label="Perform cutoff analysis" help="While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, --min-len and --max-gap may affect the results. Default=False (--cutoff-analysis)"/>
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27 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by UCSC Genome Browser (--no-trackline)"/>
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28 </inputs>
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29 <outputs>
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30 <data name="outfile" format="bedgraph" 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="bdgpeakcall_input.bdg" ftype="bedgraph" />
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35 <param name="cutoff" value="5.0"/>
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36 <param name="minlen" value="200"/>
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37 <param name="maxgap" value="30"/>
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38 <output name="outfile">
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39 <assert_contents>
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40 <has_text text="chrV" />
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41 </assert_contents>
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42 </output>
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43 </test>
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44 <test>
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45 <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
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46 <param name="cutoff" value="5.0"/>
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47 <param name="minlen" value="200"/>
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48 <param name="maxgap" value="30"/>
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49 <param name="cutoff_analysis" value="true" />
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50 <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/>
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51 </test>
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52 </tests>
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53 <help>
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54 <![CDATA[
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55 **What it does**
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56
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57 This is **bdgpeakcall** utility from the MACS2_ Package. It calls peaks from bedGraph output.
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58
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59 .. _MACS2: https://github.com/taoliu/MACS
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62 @citation@
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63 ]]>
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64 </help>
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65 <expand macro="citations" />
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66 </tool>