Mercurial > repos > xiaoyi-cao > bedtools_annotate
comparison annotateBedWrapper.xml @ 0:22e0f531e390 draft
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| author | xiaoyi-cao |
|---|---|
| date | Sun, 02 Dec 2012 15:45:34 -0500 |
| parents | |
| children | bfb51c7bfa8a |
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| -1:000000000000 | 0:22e0f531e390 |
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| 1 <tool id="annotateBed" name="Annotates"> | |
| 2 | |
| 3 <description> the depth & breadth of coverage of features from multiple files | |
| 4 </description> | |
| 5 | |
| 6 <requirements> | |
| 7 <requirement type="binary">annotateBed</requirement> | |
| 8 <requirement type="package">bedtools</requirement> | |
| 9 </requirements> | |
| 10 | |
| 11 <command> | |
| 12 annotateBed | |
| 13 $countflag | |
| 14 -i '$inputRegion' | |
| 15 -names | |
| 16 #for $i, $s in enumerate($annotateColumn) | |
| 17 '${s.colname}' | |
| 18 #end for | |
| 19 -files | |
| 20 #for $i, $s in enumerate($annotateColumn) | |
| 21 '${s.colfile}' | |
| 22 #end for | |
| 23 > '$output' | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 | |
| 28 <param format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" /> | |
| 29 <param name="countflag" type="select" label="What to report in the output: "> | |
| 30 <option value="-counts" selected="true">the count of features in each file that overlap the regions</option> | |
| 31 <option value="">fraction of the region covered by each feature</option> | |
| 32 <option value="-both">Report the counts followed by the % coverage</option> | |
| 33 </param> | |
| 34 <repeat name="annotateColumn" title="Column"> | |
| 35 <param name="colname" type="text" label="Feature name" /> | |
| 36 <param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" /> | |
| 37 </repeat> | |
| 38 | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format="bed" name="output" label="${inputRegion.name} annotated" /> | |
| 42 </outputs> | |
| 43 | |
| 44 <help> | |
| 45 | |
| 46 **What it does** | |
| 47 | |
| 48 This tool is used to annotate the regions in a bed file with features provided in multiple BED files. | |
| 49 | |
| 50 ..class:: warningmark | |
| 51 | |
| 52 This tool requires that bedtools__ has been installed on your system. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 </help> | |
| 57 | |
| 58 </tool> |