Mercurial > repos > iuc > macs2
comparison macs2_bdgdiff.xml @ 33:c82a1f154c60 draft
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| author | iuc |
|---|---|
| date | Tue, 28 Apr 2015 22:56:08 -0400 |
| parents | |
| children | 8c8ae1e19b10 |
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| 32:a2b093982c38 | 33:c82a1f154c60 |
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| 1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0"> | |
| 2 <description>Differential peak detection based on paired four bedgraph files</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>macs2_macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 macs2 bdgdiff | |
| 10 --t1 "${ infile_pileup_cond1 }" | |
| 11 --t2 "${ infile_pileup_cond2 }" | |
| 12 --c1 "${ infile_control_cond1 }" | |
| 13 --c2 "${ infile_control_cond2 }" | |
| 14 --cutoff "${ cutoff }" | |
| 15 --min-len "${ minlen }" | |
| 16 --depth1 "${ depth1 }" | |
| 17 --depth2 "${ depth2 }" | |
| 18 --max-gap "${ maxgap }" | |
| 19 --o-prefix MACS2 | |
| 20 | |
| 21 </command> | |
| 22 <expand macro="stdio" /> | |
| 23 <inputs> | |
| 24 <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" /> | |
| 25 <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" /> | |
| 26 | |
| 27 <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" /> | |
| 28 <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" /> | |
| 29 | |
| 30 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/> | |
| 31 <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/> | |
| 32 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="default: 1 (--depth1)" /> | |
| 33 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" /> | |
| 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)." /> | |
| 35 | |
| 36 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs"> | |
| 37 <option value="--ofile-cond1">Unique regions in condition 1</option> | |
| 38 <option value="--ofile-cond2">Unique regions in condition 2</option> | |
| 39 <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option> | |
| 40 <validator type="no_options" message="Please select at least one output file." /> | |
| 41 </param> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data name="output_cond1" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 1)"> | |
| 45 <filter>'--ofile-cond1' in outputs</filter> | |
| 46 </data> | |
| 47 <data name="output_cond2" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 2)"> | |
| 48 <filter>'--ofile-cond2' in outputs</filter> | |
| 49 </data> | |
| 50 <data name="output_both" format="bed" from_work_dir="MACS2_common.bed" label="${tool.name} on ${on_string} (both)"> | |
| 51 <filter>'--ofile-both-conditions' in outputs</filter> | |
| 52 </data> | |
| 53 </outputs> | |
| 54 <tests> | |
| 55 <!-- we need a second condition here --> | |
| 56 <!-- | |
| 57 <test> | |
| 58 | |
| 59 <param name="infile_control_cond1" value="Control_200K.bed" ftype="bed"/> | |
| 60 <param name="infile_control_cond2" value="Control_200K.bed" ftype="bed"/> | |
| 61 <param name="infile_pileup_cond1" value="ChIP_200K.bed" ftype="bed"/> | |
| 62 <param name="infile_pileup_cond2" value="ChIP_200K.bed" ftype="bed"/> | |
| 63 <param name="cutoff" value="1.0"/> | |
| 64 <param name="minlen" value="200"/> | |
| 65 <param name="depth1" value="1"/> | |
| 66 <param name="depth2" value="1"/> | |
| 67 <param name="maxgap" value="100"/> | |
| 68 <param name="outputs" value="-ofile-cond1,-ofile-cond2,-ofile-both-conditions"/> | |
| 69 <output name="output_cond1" file=""/> | |
| 70 <output name="output_cond2" file=""/> | |
| 71 <output name="output_both" file=""/> | |
| 72 </test> | |
| 73 --> | |
| 74 </tests> | |
| 75 <help> | |
| 76 **What it does** | |
| 77 | |
| 78 bdgdiff from macs2 | |
| 79 | |
| 80 | |
| 81 @citation@ | |
| 82 </help> | |
| 83 <expand macro="citations" /> | |
| 84 </tool> |