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1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0">
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2 <description>Differential peak detection based on paired four bedgraph files</description>
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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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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 --max-gap "${ maxgap }"
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19 --o-prefix MACS2
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20
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21 </command>
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22 <expand macro="stdio" />
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23 <inputs>
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24 <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
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25 <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
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26
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27 <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" />
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28 <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" />
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29
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30 <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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31 <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/>
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32 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="default: 1 (--depth1)" />
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33 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" />
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34 <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default: 100 (-g)." />
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35
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36 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
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37 <option value="--ofile-cond1">Unique regions in condition 1</option>
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38 <option value="--ofile-cond2">Unique regions in condition 2</option>
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39 <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
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40 <validator type="no_options" message="Please select at least one output file." />
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41 </param>
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42 </inputs>
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43 <outputs>
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44 <data name="output_cond1" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 1)">
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45 <filter>'--ofile-cond1' in outputs</filter>
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46 </data>
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47 <data name="output_cond2" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 2)">
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48 <filter>'--ofile-cond2' in outputs</filter>
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49 </data>
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50 <data name="output_both" format="bed" from_work_dir="MACS2_common.bed" label="${tool.name} on ${on_string} (both)">
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51 <filter>'--ofile-both-conditions' in outputs</filter>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <!-- we need a second condition here -->
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56 <!--
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57 <test>
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58
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59 <param name="infile_control_cond1" value="Control_200K.bed" ftype="bed"/>
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60 <param name="infile_control_cond2" value="Control_200K.bed" ftype="bed"/>
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61 <param name="infile_pileup_cond1" value="ChIP_200K.bed" ftype="bed"/>
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62 <param name="infile_pileup_cond2" value="ChIP_200K.bed" ftype="bed"/>
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63 <param name="cutoff" value="1.0"/>
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64 <param name="minlen" value="200"/>
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65 <param name="depth1" value="1"/>
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66 <param name="depth2" value="1"/>
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67 <param name="maxgap" value="100"/>
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68 <param name="outputs" value="-ofile-cond1,-ofile-cond2,-ofile-both-conditions"/>
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69 <output name="output_cond1" file=""/>
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70 <output name="output_cond2" file=""/>
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71 <output name="output_both" file=""/>
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72 </test>
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73 -->
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74 </tests>
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75 <help>
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76 **What it does**
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77
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78 bdgdiff from macs2
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79
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80
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81 @citation@
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82 </help>
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83 <expand macro="citations" />
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84 </tool>
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