Mercurial > repos > xiaoyi-cao > annotatebed
comparison annotateBedWrapper.xml @ 0:0cba7d8f48ab draft
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| author | xiaoyi-cao |
|---|---|
| date | Sun, 02 Dec 2012 12:11:45 -0500 |
| parents | |
| children | 21a126fcfd13 |
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| -1:000000000000 | 0:0cba7d8f48ab |
|---|---|
| 1 <tool id="annotateBed" name="annotateBed"> | |
| 2 | |
| 3 <description>TYPE_DESCRIPTION_HERE</description> | |
| 4 | |
| 5 <command interpreter="bash"> | |
| 6 names="" | |
| 7 inputfiles="" | |
| 8 #for $i, $s in enumerate($annotateColumn) | |
| 9 names=$names + ${s.colname} + " " | |
| 10 inputfiles=$inputfiles+ ${s.colfile} + " " | |
| 11 #end for | |
| 12 bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles | |
| 13 </command> | |
| 14 | |
| 15 <inputs> | |
| 16 | |
| 17 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" /> | |
| 18 <param format="bed" name="inputRegion" type="data" label="The region to be annotated" /> | |
| 19 <repeat name="annotateColumn" title="Column"> | |
| 20 <param name="colname" type="text" label="Column name" /> | |
| 21 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" /> | |
| 22 </repeat> | |
| 23 | |
| 24 </inputs> | |
| 25 | |
| 26 <outputs> | |
| 27 | |
| 28 <data format="bed" name="output" /> | |
| 29 | |
| 30 </outputs> | |
| 31 | |
| 32 <help> | |
| 33 | |
| 34 .. class:: infomark | |
| 35 | |
| 36 IMPORTANT INFORMATION | |
| 37 | |
| 38 ---- | |
| 39 | |
| 40 WRITE HELP HERE | |
| 41 | |
| 42 </help> | |
| 43 | |
| 44 </tool> |