Mercurial > repos > kpbioteam > chipeakanno_annopeaks
comparison chipeakanno_annopeaks.xml @ 11:8a91d82803a9 draft
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 1d355e9a8d667b026e22e5f8956f19199c5af880
| author | kpbioteam |
|---|---|
| date | Sat, 23 Jun 2018 06:15:12 -0400 |
| parents | b1274d30071e |
| children |
comparison
equal
deleted
inserted
replaced
| 10:b1274d30071e | 11:8a91d82803a9 |
|---|---|
| 7 </requirements> | 7 </requirements> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 Rscript ${__tool_directory__}/chipeakanno_annopeaks.R "$input1" "$input2" "$input3" "$input4" "$input5" "$output1" | 9 Rscript ${__tool_directory__}/chipeakanno_annopeaks.R "$input1" "$input2" "$input3" "$input4" "$input5" "$output1" |
| 10 ]]></command> | 10 ]]></command> |
| 11 <inputs> | 11 <inputs> |
| 12 <param type="data" name="input1" format="bedgraph"/> | 12 <param type="data" name="input1" format="bedgraph" label="Differentially Methylated Data"/> |
| 13 <param name="input2" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand"> | 13 <param name="input2" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand"> |
| 14 <option value="startSite">startSite</option> | 14 <option value="startSite">startSite</option> |
| 15 <option value="endSite">endSite</option> | 15 <option value="endSite">endSite</option> |
| 16 <option value="fullRange">fullRange</option> | 16 <option value="fullRange">fullRange</option> |
| 17 <option value="nearestBiDirectionalPromoters">nearestBiDirectionalPromoters</option> | 17 <option value="nearestBiDirectionalPromoters">nearestBiDirectionalPromoters</option> |
| 20 <param name="input4" type="text" value="3000" label="bindingRegionEnd" help="e.g. to obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = nearestBiDirectionalPromoters and bindingRegion = c(-5000, 3000)"/> | 20 <param name="input4" type="text" value="3000" label="bindingRegionEnd" help="e.g. to obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = nearestBiDirectionalPromoters and bindingRegion = c(-5000, 3000)"/> |
| 21 | 21 |
| 22 <param name="input5" type="text" value="1" label="Additional Column of Score" help="Position of Additional Column of the Score" /> | 22 <param name="input5" type="text" value="1" label="Additional Column of Score" help="Position of Additional Column of the Score" /> |
| 23 </inputs> | 23 </inputs> |
| 24 <outputs> | 24 <outputs> |
| 25 <data name="output1" format="txt" /> | 25 <data name="output1" format="txt" label="Table of Annotated Peaks"/> |
| 26 </outputs> | 26 </outputs> |
| 27 <tests> | 27 <tests> |
| 28 <test> | 28 <test> |
| 29 <param name="input1" value="dmr.bedgraph"/> | 29 <param name="input1" value="dmr.bedgraph"/> |
| 30 <param name="input2" value="startSite"/> | 30 <param name="input2" value="startSite"/> |