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1 <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="2.0.10.0">
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2 <description>Deduct noise by comparing two signal tracks in bedGraph</description>
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1
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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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0
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8 <command>
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9 macs2 bdgcmp
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10 -t $input_treatment_file
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11 -c $input_control_file
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12
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13 -m $bdgcmp_options.bdgcmp_options_selector
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14 #if $bdgcmp_options.bdgcmp_options_selector in ['FE', 'logFR', 'logLR']:
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15 -p $pseudocount
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16 #end if
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17 --ofile $ofile
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18
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19 </command>
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20 <expand macro="stdio" />
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21 <inputs>
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22 <!--experiment name and option of selecting paired or single end will always be present-->
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23 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
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24
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25 <param name="input_treatment_file" type="data" format="bedgraph" label="Treatment bedGraph file" />
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26 <param name="input_control_file" type="data" format="bedgraph" label="Control bedGraph file" />
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27
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28 <conditional name="bdgcmp_options">
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29 <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">
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30 <option value="ppois">Poisson Pvalue (-log10 (pvalue) form) using control as lambda and treatment as observation</option>
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31 <option value="qpois">q-value through a BH process for poisson pvalues</option>
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32 <option value="subtract">subtraction from treatment</option>
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33 <option value="logFE">log10 fold enrichment</option>
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34 <option value="FE">linear scale fold enrichment</option>
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35 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model</option>
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36 <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models and open chromatin model</option>
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37 </param>
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38 <when value="FE">
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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="logLR">
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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="logFE">
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45 <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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46 </when>
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47 </conditional>
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48
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49 </inputs>
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50
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51 <outputs>
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52 <data name="ofile" format="bedgraph" label="${tool.name} on ${on_string}" />
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53 </outputs>
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54 <tests>
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55 <!--none yet for macs2-->
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
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61 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
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62 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
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63 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
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64
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65 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
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66
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67 ------
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68
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69 **Usage**
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70
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71 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
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72
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73 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
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74
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75
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9
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76 @citation@
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0
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77 </help>
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78 </tool>
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