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annotate macs2_bdgcmp.xml @ 10:f0b351e734b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e9415c8ba21c77f848a57d60ee6be78dff4b49a6
author iuc
date Wed, 31 Jan 2018 15:12:13 -0500
parents acbd3fb47f90
children 640d3af5d833
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1 <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0">
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2 <description>Deduct noise by comparing two signal tracks in bedGraph</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 bdgcmp
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12 -t '${ infile_treatment }'
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13 -c '${ infile_control }'
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15 -m '${ bdgcmp_options.bdgcmp_options_selector }'
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16 #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
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17 -p '${ bdgcmp_options.pseudocount }'
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18 #end if
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19 -o '${ outfile }'
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20 ]]></command>
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21 <inputs>
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22 <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
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23 <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />
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25 <conditional name="bdgcmp_options">
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26 <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value" help="Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default=ppois (--method).">
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27 <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
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28 <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
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29 <option value="subtract">subtraction from treatment (subtract)</option>
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30 <option value="logFE">log10 fold enrichment (logFE)</option>
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31 <option value="FE">linear scale fold enrichment (FE)</option>
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32 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
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33 <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
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34 </param>
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35 <when value="FE">
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36 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
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37 </when>
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38 <when value="logLR">
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39 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
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40 </when>
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41 <when value="logFE">
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42 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
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43 </when>
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44 <when value="ppois"/>
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45 <when value="qpois"/>
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46 <when value="subtract"/>
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47 <when value="slogLR"/>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="infile_control" value="bdgcmp_input_control.bdg" ftype="bedgraph"/>
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56 <param name="infile_treatment" value="bdgcmp_input_treatment.bdg" ftype="bedgraph"/>
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57 <param name="bdgcmp_options_selector" value="ppois"/>
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58 <output name="outfile" file="bdgcmp_output.bdg"/>
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59 </test>
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60 </tests>
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61 <help>
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62 <![CDATA[
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63 **What it does**
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64
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65 This is **bdgcmp** utility from the MACS2_ Package. It is designed to deduct noise by comparing two signal tracks in bedGraph.
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66
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67 .. _MACS2: https://github.com/taoliu/MACS
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69 @citation@
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70 ]]>
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71 </help>
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72 <expand macro="citations" />
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73 </tool>