annotate genetrack.xml @ 1:df7ac50ade5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 6cd0f93f4eb8649802683ae4c189c8ad48827a49
author iuc
date Fri, 13 Jan 2017 10:20:48 -0500
parents 25cd59a002d9
children b41a4bb828a3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
1
df7ac50ade5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 6cd0f93f4eb8649802683ae4c189c8ad48827a49
iuc
parents: 0
diff changeset
2 <tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.1">
0
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
3 <description>peak predictor</description>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
4 <macros>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
5 <import>genetrack_macros.xml</import>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
6 </macros>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
7 <expand macro="requirements" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
8 <command>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
9 python $__tool_directory__/genetrack.py
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
10 --input_format $input_format_cond.input_format
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
11 #for $i in $input_format_cond.input:
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
12 --input "${i}" "${i.hid}"
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
13 #end for
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
14 --sigma $sigma
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
15 --exclusion $exclusion
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
16 --up_width $up_width
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
17 --down_width $down_width
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
18 --filter $filter
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
19 </command>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
20 <inputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
21 <conditional name="input_format_cond">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
22 <param name="input_format" type="select" label="Format of files for conversion">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
23 <option value="scidx" selected="True">ScIdx</option>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
24 <option value="gff">Gff</option>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
25 </param>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
26 <when value="scidx">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
27 <param name="input" type="data" format="scidx" multiple="True" label="Predict peaks on" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
28 </when>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
29 <when value="gff">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
30 <param name="input" type="data" format="gff" multiple="True" label="Predict peaks on" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
31 </when>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
32 </conditional>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
33 <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." />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
34 <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." />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
35 <param name="up_width" type="integer" value="10" min="0" label="Exclusion zone of upstream called peaks" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
36 <param name="down_width" type="integer" value="10" min="0" label="Exclusion zone of downstream called peaks" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
37 <param name="filter" type="integer" value="1" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
38 </inputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
39 <outputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
40 <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
41 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
42 </collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
43 </outputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
44 <tests>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
45 <test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
46 <param name="input" value="genetrack_input2.gff" ftype="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
47 <param name="input_format" value="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
48 <param name="sigma" value="5" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
49 <param name="exclusion" value="20" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
50 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
51 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
52 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
53 <output_collection name="genetrack_output" type="list">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
54 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
55 </output_collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
56 </test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
57 <test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
58 <param name="input" value="genetrack_input3.scidx" ftype="scidx" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
59 <param name="input_format" value="scidx" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
60 <param name="sigma" value="5" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
61 <param name="exclusion" value="20" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
62 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
63 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
64 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
65 <output_collection name="genetrack_output" type="list">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
66 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
67 </output_collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
68 </test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
69 <test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
70 <param name="input" value="genetrack_input_unsorted4.gff" ftype="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
71 <param name="input_format" value="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
72 <param name="sigma" value="5" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
73 <param name="exclusion" value="20" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
74 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
75 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
76 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
77 <output_collection name="genetrack_output" type="list">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
78 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
79 </output_collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
80 </test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
81 </tests>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
82 <help>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
83 **What it does**
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
84
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
85 GeneTrack separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. The way that GeneTrack
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
86 works is to replace each tag with a probabilistic distribution of occurrences for that tag at and around its mapped
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
87 genomic coordinate. The distance decay of the probabilistic distribution is set by adjusting the value of the
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
88 tool's **Sigma to use when smoothing reads** parameter. GeneTrack then sums the distribution over all mapped
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
89 tags. This results in a smooth continuous trace that can be globally broadened or tightened by adjusting the
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
90 sigma value. GeneTrack starts with the highest smoothed peak first, treating each strand separately if indicated
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
91 by the data, then sets up an exclusion zone (centered over the peak) defined by the value of the **Peak exclusion
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
92 zone** parameter (see figure). The exclusion zone prevents any secondary peaks from being called on the same strand
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
93 within that exclusion zone. In rare cases, it may be desirable to set different exclusion zones upstream (more 5’)
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
94 versus downstream (more 3’) of the peak.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
95
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
96 .. image:: $PATH_TO_IMAGES/genetrack.png
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
97
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
98 GeneTrack continues through the data in order of peak height, until no other peaks are found, and in principle will
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
99 call a peak at a single isolated tag, if no filter is set using the tool's **Absolute read filter** parameter. A
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
100 filter value of 1 means that it will stop calling peaks when the tag count in the peak hits 1 (so single tag peaks
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
101 will be excluded in this case). GeneTrack outputs **chrom** (chromosome number), **strand** (+/W or -/C strand),
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
102 **start** (lower coordinate of exclusion zone), **end** (higher coordinate of exclusion zone), and **value** (peak
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
103 height). Genetrack's GFF output reports the start (lower coordinate) and end (higher coordinate) of the exclusion
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
104 zone.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
105
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
106 In principle, the width of the exclusion zone may be as large as the DNA region occupied by the native protein plus
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
107 a steric exclusion zone between the protein and the exonuclease. On the other hand the site might be considerably
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
108 smaller if the protein is in a denatured state during exonuclease digestion (since it is pre-treated with SDS).
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
109
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
110 In general, higher resolution data or smaller binding site size data should use smaller sigma values. Large binding
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
111 site size data such as 147 bp nucleosomal DNA use a larger sigma value like 20 (-s 20). For transcription factors
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
112 mapped by ChIP-exo, sigma may initially be set at 5, and the exclusion zone set at 20 (-s 5 –e 20). Sigma is typically
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
113 varied between ~3 and ~20. Too high of a sigma value may merge two independent nearby binding events. This may be
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
114 desirable if closely bound factors are not distinguishable. Too low of a sigma value will cause some tags that
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
115 contribute to a binding event to be excluded, because they may not be located sufficiently close to the main peak.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
116 If alternative (mutually exclusive) binding is expected for two overlapping sites, and these sites are to be
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
117 independently recorded, then an empirically determined smaller exclusion zone width is set. Thus the value of sigma
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
118 is set empirically for each mapped factor, depending upon the resolution and binding site size of the binding event.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
119
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
120 It might make sense to exclude peaks that have only a single tag, where -F 1 is used, or have their tags located on
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
121 only a single coordinate (called Singletons, where stddev=0 in the output file). However, low coverage datasets might
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
122 be improved by including them, if additional analysis (e.g., motif discovery) validates them. In addition, idealized
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
123 action of the exonuclease in ChIP-exo might place all tags for a peak on a single coordinate.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
124
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
125 -----
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
126
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
127 **Options**
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
128
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
129 * **Sigma to use when smoothing reads** - Smooths clusters of tags via a Gaussian distribution.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
130 * **Peak exclusion zone** - Exclusion zone around each peak, eliminating all other peaks on the same strand that are within a ± bp distance of the peak.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
131 * **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
132 * **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
133 * **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
134
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
135 -----
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
136
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
137 **Output gff Columns**
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
138
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
139 1. Chromosome
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
140 2. Script
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
141 3. Placeholder (no meaning)
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
142 4. Start of peak exclusion zone (-e 20)
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
143 5. End of peak exclusion zone
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
144 6. Tag sum (not peak height or area under curve, which LionDB provides)
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
145 7. Strand
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
146 8. Placeholder (no meaning)
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
147 9. Attributes (standard deviation of reads located within exclusion zone) = fuzziness of peak
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
148
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
149 -----
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
150
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
151 **Considerations**
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
152
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
153 In principle, the width of the exclusion zone may be as large as the DNA region occupied by the native protein
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
154 plus a steric exclusion zone between the protein and the exonuclease. On the other hand the site might be considerably
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
155 smaller if the protein is in a denatured state during exonuclease digestion (since it is pre-treated with SDS).
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
156
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
157 In general, higher resolution data or smaller binding site size data should use smaller sigma values. Large binding site
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
158 size data such as 147 bp nucleosomal DNA use a larger sigma value like 20 (-s 20). For transcription factors mapped by
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
159 ChIP-exo, sigma may initially be set at 5, and the exclusion zone set at 20 (-s 5 –e 20). Sigma is typically varied
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
160 between ~3 and ~20. Too high of a sigma value may merge two independent nearby binding events. This may be desirable if
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
161 closely bound factors are not distinguishable. Too low of a sigma value will cause some tags that contribute to a binding
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
162 event to be excluded, because they may not be located sufficiently close to the main peak. If alternative (mutually
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
163 exclusive) binding is expected for two overlapping sites, and these sites are to be independently recorded, then an
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
164 empirically determined smaller exclusion zone width is set. Thus, the value of sigma is set empirically for each mappedfactor depending upon the resolution and binding site size of the binding event.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
165
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
166 It might make sense to exclude peaks that have only a single tag, where -F 1 is used, or have their tags located on only
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
167 a single coordinate (called Singletons, where stddev=0 in the output file). However, low coverage datasets might be
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
168 improved by including them, if additional analysis (e.g., motif discovery) validates them. In addition, idealized action
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
169 of the exonuclease in ChIP-exo might place all tags for a peak on a single coordinate.
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
170
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
171 </help>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
172 <expand macro="citations" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
173 </tool>