Mercurial > repos > miller-lab > genome_diversity
comparison find_intervals.xml @ 21:d6b961721037
Miller Lab Devshed version 4c04e35b18f6
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Mon, 05 Nov 2012 12:44:17 -0500 |
parents | 8ae67e9fb6ff |
children | 95a05c1ef5d5 |
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20:8a4b8efbc82c | 21:d6b961721037 |
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20 | 20 |
21 "$out_format" | 21 "$out_format" |
22 </command> | 22 </command> |
23 | 23 |
24 <inputs> | 24 <inputs> |
25 <param name="input" type="data" format="tabular" label="Input"> | 25 <param name="input" type="data" format="tabular" label="Dataset"> |
26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | 26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> |
27 </param> | 27 </param> |
28 | 28 |
29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/> | 29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/> |
30 | 30 |
31 <conditional name="cutoff"> | 31 <conditional name="cutoff"> |
32 <param name="type" type="select" label="Cutoff type"> | 32 <param name="type" type="select" label="Score-shift type"> |
33 <option value="percentage">percentage</option> | 33 <option value="percentage">percentage</option> |
34 <option value="value">value</option> | 34 <option value="value">value</option> |
35 </param> | 35 </param> |
36 <when value="percentage"> | 36 <when value="percentage"> |
37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/> | 37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage score-shift"/> |
38 </when> | 38 </when> |
39 <when value="value"> | 39 <when value="value"> |
40 <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/> | 40 <param name="cutoff_val" type="float" value="0.0" label="Value score-shift"/> |
41 </when> | 41 </when> |
42 </conditional> | 42 </conditional> |
43 | 43 |
44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/> | 44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/> |
45 | 45 |
46 <param name="out_format" type="select" format="integer" label="Report individual positions"> | 46 <param name="out_format" type="select" format="integer" label="Report individual positions"> |
47 <option value="0" selected="true">No</option> | 47 <option value="0" selected="true">no</option> |
48 <option value="1">Yes</option> | 48 <option value="1">yes</option> |
49 </param> | 49 </param> |
50 | 50 |
51 <conditional name="override_metadata"> | 51 <conditional name="override_metadata"> |
52 <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you need to choose the columns if the input dataset is not gd_snp"> | 52 <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you must choose the columns if the input dataset is not gd_snp."> |
53 <option value="0" selected="true">No, get columns from metadata</option> | 53 <option value="0" selected="true">no, get columns from metadata</option> |
54 <option value="1" >Yes, choose columns</option> | 54 <option value="1" >yes, choose columns here</option> |
55 </param> | 55 </param> |
56 <when value="0" /> | 56 <when value="0" /> |
57 <when value="1"> | 57 <when value="1"> |
58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure the build in the metadata is the same as using here."/> | 58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure this corresponds to the build recorded in the metadata."/> |
59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero or one based positions will work"/> | 59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero-based or one-based positions will work."/> |
60 </when> | 60 </when> |
61 </conditional> | 61 </conditional> |
62 </inputs> | 62 </inputs> |
63 | 63 |
64 <outputs> | 64 <outputs> |
103 if the dataset is not also gd_snp format, specifies | 103 if the dataset is not also gd_snp format, specifies |
104 the columns containing chromosome, position, and scores (such as an Fst-value for the SNP). | 104 the columns containing chromosome, position, and scores (such as an Fst-value for the SNP). |
105 For gd_snp format the metadata can be used to specify the chromosome and | 105 For gd_snp format the metadata can be used to specify the chromosome and |
106 position. | 106 position. |
107 Other inputs include | 107 Other inputs include |
108 a percentage or raw score for the "cutoff" which should be greater than the | 108 a percentage or raw score for the "score-shift" which should be greater than the |
109 average value for the scores column. A higher value will give smaller intervals | 109 average value for the scores column. A higher value will give smaller intervals |
110 in the output. | 110 in the output. |
111 If a percentage (e.g. 95%) is specified | 111 If a percentage (e.g. 95%) is specified |
112 then that percentile of the scores is used as the cutoff; | 112 then that percentile of the scores is used as the shift; |
113 percentile may not work well if many rows or SNPs have the same score | 113 percentile may not work well if many rows or SNPs have the same score |
114 (in that case use a raw score). The program subtracts the | 114 (in that case use a raw score). The program subtracts the |
115 cutoff from every score, then finds genomic intervals (i.e., consecutive runs | 115 shift from every score, then finds genomic intervals (i.e., consecutive runs |
116 of SNPs) whose total score cannot be increased by adding or subtracting one | 116 of SNPs) whose total score cannot be increased by adding or subtracting one |
117 or more adjusted scores at the ends of the interval. | 117 or more adjusted scores at the ends of the interval. |
118 Another input is the number of times the | 118 Another input is the number of times the |
119 data should be randomized (only intervals with score exceeding the maximum for | 119 data should be randomized (only intervals with score exceeding the maximum for |
120 the randomized data are reported). | 120 the randomized data are reported). |