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comparison genetrack.xml @ 11:497e3274f70b draft

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author greg
date Wed, 02 Dec 2015 16:15:05 -0500
parents fa85ca6c9cf8
children cd105fdfb0da
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10:1a9f1a4fa36c 11:497e3274f70b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="genetrack" name="Genetrack" version="@WRAPPER_VERSION@.0"> 2 <tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.0">
3 <description>peak predictor</description> 3 <description>peak predictor</description>
4 <macros> 4 <macros>
5 <import>genetrack_macros.xml</import> 5 <import>genetrack_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
20 --sigma $sigma 20 --sigma $sigma
21 --exclusion $exclusion 21 --exclusion $exclusion
22 --up_width $up_width 22 --up_width $up_width
23 --down_width $down_width 23 --down_width $down_width
24 --filter $filter 24 --filter $filter
25 --chunk_size $chunk_size
26 </command> 25 </command>
27 <inputs> 26 <inputs>
28 <conditional name="input_format_cond"> 27 <conditional name="input_format_cond">
29 <param name="input_format" type="select" label="Format of files for conversion"> 28 <param name="input_format" type="select" label="Format of files for conversion">
30 <option value="scidx" selected="True">ScIdx</option> 29 <option value="scidx" selected="True">ScIdx</option>
40 <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." /> 39 <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
41 <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." /> 40 <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
42 <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" /> 41 <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" />
43 <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" /> 42 <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" />
44 <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." /> 43 <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
45 <param name="chunk_size" type="integer" value="10" min="1" label="Chunk each chromosome into" help="Value is millions of base pairs where each size increment uses about 20MB of memory." />
46 </inputs> 44 </inputs>
47 <outputs> 45 <outputs>
48 <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}"> 46 <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
49 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" /> 47 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
50 </collection> 48 </collection>
56 <param name="sigma" value="5" /> 54 <param name="sigma" value="5" />
57 <param name="exclusion" value="20" /> 55 <param name="exclusion" value="20" />
58 <param name="up_width" value="10" /> 56 <param name="up_width" value="10" />
59 <param name="down_width" value="10" /> 57 <param name="down_width" value="10" />
60 <param name="filter" value="3" /> 58 <param name="filter" value="3" />
61 <param name="chunk_size" value="10" />
62 <output_collection name="genetrack_output" type="list"> 59 <output_collection name="genetrack_output" type="list">
63 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" /> 60 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
64 </output_collection> 61 </output_collection>
65 </test> 62 </test>
66 <test> 63 <test>
69 <param name="sigma" value="5" /> 66 <param name="sigma" value="5" />
70 <param name="exclusion" value="20" /> 67 <param name="exclusion" value="20" />
71 <param name="up_width" value="10" /> 68 <param name="up_width" value="10" />
72 <param name="down_width" value="10" /> 69 <param name="down_width" value="10" />
73 <param name="filter" value="3" /> 70 <param name="filter" value="3" />
74 <param name="chunk_size" value="10" />
75 <output_collection name="genetrack_output" type="list"> 71 <output_collection name="genetrack_output" type="list">
76 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" /> 72 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" />
77 </output_collection> 73 </output_collection>
78 </test> 74 </test>
79 <test> 75 <test>
82 <param name="sigma" value="5" /> 78 <param name="sigma" value="5" />
83 <param name="exclusion" value="20" /> 79 <param name="exclusion" value="20" />
84 <param name="up_width" value="10" /> 80 <param name="up_width" value="10" />
85 <param name="down_width" value="10" /> 81 <param name="down_width" value="10" />
86 <param name="filter" value="3" /> 82 <param name="filter" value="3" />
87 <param name="chunk_size" value="10" />
88 <output_collection name="genetrack_output" type="list"> 83 <output_collection name="genetrack_output" type="list">
89 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" /> 84 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" />
90 </output_collection> 85 </output_collection>
91 </test> 86 </test>
92 </tests> 87 </tests>
93 <help> 88 <help>
94 **What it does** 89 **What it does**
95 90
96 Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads. 91 Genetrack supports ChIP experiments. The peak caller takes a standard set of data on both the sense and
97 It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final 92 antisense strands (ScIdx format) and smooths their relative reads. It then predicts the peaks present in
98 reads from surrounding reads. Finally, it ensures each peak is above a threshold and that two peaks are not 93 the smoothed dataset and uses those peak locations to find the maximal non-overlapping subset. It then
94 selects the highest peak and establishes an exclusion zone, and no other predicted peaks will be reported
95 within the exclusion zone. Finally, it ensures each peak is above a threshold and that two peaks are not
99 too close to each other. 96 too close to each other.
100 97
101 ----- 98 -----
102 99
103 **Options** 100 **Options**
105 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks. 102 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
106 * **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called. 103 * **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
107 * **Upstream width of called peaks** - Upstream width of called peaks. 104 * **Upstream width of called peaks** - Upstream width of called peaks.
108 * **Downstream width of called peaks** - Downstream width of called peaks. 105 * **Downstream width of called peaks** - Downstream width of called peaks.
109 * **Filter** - Absolute read filter. Restricts output to only peaks with larger peak height. 106 * **Filter** - Absolute read filter. Restricts output to only peaks with larger peak height.
110 * **Chunk each chromosome into** - Size, in millions of base pairs, to chunk each chromosome when processing. Each 1 million size uses approximately 20MB of memory.
111 </help> 107 </help>
112 <expand macro="citations" /> 108 <expand macro="citations" />
113 </tool> 109 </tool>