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1 <tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0">
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2 <description>based on paired four bedgraph files</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 bdgdiff
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10 --t1 $infile_pileup_cond1
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11 --t2 $infile_pileup_cond2
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12 --c1 $infile_control_cond1
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13 --c2 $infile_control_cond2
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14 --cutoff $cutoff
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15 --min-len $minlen
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16 --depth1 $depth1
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17 --depth2 $depth2
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18
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19 # Why does #if '--ofile-cond1' in $outputs not work?
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20 #if '--ofile-cond1' in str($outputs).split(','):
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21 --ofile-cond1 $output_cond1
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22 #end if
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23
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24 #if '--ofile-cond2' in str($outputs).split(','):
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25 --ofile-cond2 $output_cond2
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26 #end if
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27
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28 #if '--ofile-both-conditions' in str($outputs).split(','):
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29 --ofile-both-conditions $output_both
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30 #end if
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31 </command>
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32 <inputs>
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33 <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
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34 <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
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35
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36 <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" />
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37 <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" />
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38
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1
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39 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/>
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40 <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/>
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41 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default: 1 (--depth1)" />
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42 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default: 1 (--depth2)" />
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43
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44 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
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45 <option value="--ofile-cond1">Unique regions in condition 1</option>
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46 <option value="--ofile-cond2">Unique regions in condition 2</option>
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47 <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
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48 <validator type="no_options" message="Please select at least one output file." />
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49 </param>
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50
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51 </inputs>
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52
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53 <outputs>
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54 <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (cond 1)">
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55 <filter>'--ofile-cond1' in outputs</filter>
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56 </data>
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57 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (cond 2)">
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58 <filter>'--ofile-cond2' in outputs</filter>
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59 </data>
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60 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (both)">
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61 <filter>'--ofile-both-conditions' in outputs</filter>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <!--none yet for macs2-->
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66 </tests>
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67 <help>
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68 **What it does**
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69
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70 bdgdiff from macs2
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71
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72
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73 ------
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74
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75 **Citation**
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76
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77 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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78
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79 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
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80 </help>
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81 </tool>
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