Mercurial > repos > iuc > bedtools
comparison mapBed.xml @ 3:2cd7e321d259 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 27 May 2015 12:54:35 -0400 |
| parents | 457b09031d57 |
| children | 607c0576c6ab |
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| 2:457b09031d57 | 3:2cd7e321d259 |
|---|---|
| 28 <expand macro="overlap" /> | 28 <expand macro="overlap" /> |
| 29 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" | 29 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" |
| 30 label="Require reciprocal overlap" | 30 label="Require reciprocal overlap" |
| 31 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" /> | 31 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" /> |
| 32 <expand macro="strand2" /> | 32 <expand macro="strand2" /> |
| 33 <expand macro="c_and_o_argument" /> | 33 <expand macro="c_and_o_argument"> |
| 34 <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" /> | |
| 35 </expand> | |
| 34 <expand macro="split" /> | 36 <expand macro="split" /> |
| 35 <expand macro="print_header" /> | 37 <expand macro="print_header" /> |
| 36 <conditional name="genome"> | 38 <conditional name="genome"> |
| 37 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" | 39 <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" |
| 38 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" /> | 40 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" /> |
| 47 <tests> | 49 <tests> |
| 48 <test> | 50 <test> |
| 49 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | 51 <param name="inputA" value="mapBed1.bed" ftype="bed" /> |
| 50 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | 52 <param name="inputB" value="mapBed2.bed" ftype="bed" /> |
| 51 <repeat name="c_and_o_argument_repeat"> | 53 <repeat name="c_and_o_argument_repeat"> |
| 52 <param name="cols" value="5" /> | 54 <param name="col" value="5" /> |
| 53 <param name="operation" value="mean" /> | 55 <param name="operation" value="mean" /> |
| 54 </repeat> | 56 </repeat> |
| 55 <output name="output" file="mapBed_result1.bed" ftype="bed" /> | 57 <output name="output" file="mapBed_result1.bed" ftype="bed" /> |
| 56 </test> | 58 </test> |
| 57 <test> | 59 <test> |
| 65 </test> | 67 </test> |
| 66 <test> | 68 <test> |
| 67 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | 69 <param name="inputA" value="mapBed1.bed" ftype="bed" /> |
| 68 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | 70 <param name="inputB" value="mapBed2.bed" ftype="bed" /> |
| 69 <repeat name="c_and_o_argument_repeat"> | 71 <repeat name="c_and_o_argument_repeat"> |
| 70 <param name="cols" value="5" /> | 72 <param name="col" value="5" /> |
| 71 <param name="operation" value="collapse" /> | 73 <param name="operation" value="collapse" /> |
| 72 </repeat> | 74 </repeat> |
| 73 <param name="strand" value="-S" /> | 75 <param name="strand" value="-S" /> |
| 74 <output name="output" file="mapBed_result3.bed" ftype="bed" /> | 76 <output name="output" file="mapBed_result3.bed" ftype="bed" /> |
| 75 </test> | 77 </test> |
| 76 <test> | 78 <test> |
| 77 <param name="inputA" value="mapBed1.bed" ftype="bed" /> | 79 <param name="inputA" value="mapBed1.bed" ftype="bed" /> |
| 78 <param name="inputB" value="mapBed2.bed" ftype="bed" /> | 80 <param name="inputB" value="mapBed2.bed" ftype="bed" /> |
| 79 <repeat name="c_and_o_argument_repeat"> | 81 <repeat name="c_and_o_argument_repeat"> |
| 80 <param name="cols" value="5" /> | 82 <param name="col" value="5" /> |
| 81 <param name="operation" value="collapse" /> | 83 <param name="operation" value="collapse" /> |
| 82 </repeat> | 84 </repeat> |
| 83 <param name="strand" value="-s" /> | 85 <param name="strand" value="-s" /> |
| 84 <output name="output" file="mapBed_result4.bed" ftype="bed" /> | 86 <output name="output" file="mapBed_result4.bed" ftype="bed" /> |
| 85 </test> | 87 </test> |