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comparison mapBed.xml @ 3:2cd7e321d259 draft

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Uploaded
author iuc
date Wed, 27 May 2015 12:54:35 -0400
parents 457b09031d57
children 607c0576c6ab
comparison
equal deleted inserted replaced
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>