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annotate genetrack.xml @ 0:25cd59a002d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 17:03:27 -0500
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25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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1 <?xml version="1.0"?>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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2 <tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.0">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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3 <description>peak predictor</description>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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4 <macros>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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5 <import>genetrack_macros.xml</import>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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6 </macros>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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7 <expand macro="requirements" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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8 <command>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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9 python $__tool_directory__/genetrack.py
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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11 #for $i in $input_format_cond.input:
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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12 --input "${i}" "${i.hid}"
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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13 #end for
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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14 --sigma $sigma
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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15 --exclusion $exclusion
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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16 --up_width $up_width
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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17 --down_width $down_width
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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18 --filter $filter
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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19 </command>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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20 <inputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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21 <conditional name="input_format_cond">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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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
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24 <option value="gff">Gff</option>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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25 </param>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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26 <when value="scidx">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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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
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28 </when>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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29 <when value="gff">
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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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
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31 </when>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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32 </conditional>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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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
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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
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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
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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
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38 </inputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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39 <outputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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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
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42 </collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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43 </outputs>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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44 <tests>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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45 <test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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47 <param name="input_format" value="gff" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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48 <param name="sigma" value="5" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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49 <param name="exclusion" value="20" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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50 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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51 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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52 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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53 <output_collection name="genetrack_output" type="list">
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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
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55 </output_collection>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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56 </test>
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57 <test>
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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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
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59 <param name="input_format" value="scidx" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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60 <param name="sigma" value="5" />
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61 <param name="exclusion" value="20" />
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62 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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63 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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64 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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65 <output_collection name="genetrack_output" type="list">
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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
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67 </output_collection>
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68 </test>
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69 <test>
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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
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71 <param name="input_format" value="gff" />
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72 <param name="sigma" value="5" />
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73 <param name="exclusion" value="20" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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74 <param name="up_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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75 <param name="down_width" value="10" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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76 <param name="filter" value="3" />
25cd59a002d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit e96df94dba60050fa28aaf55b5bb095717a5f260
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77 <output_collection name="genetrack_output" type="list">
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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
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79 </output_collection>
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80 </test>
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81 </tests>
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82 <help>
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83 **What it does**
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84
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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
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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
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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
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88 tool's **Sigma to use when smoothing reads** parameter. GeneTrack then sums the distribution over all mapped
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89 tags. This results in a smooth continuous trace that can be globally broadened or tightened by adjusting the
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90 sigma value. GeneTrack starts with the highest smoothed peak first, treating each strand separately if indicated
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91 by the data, then sets up an exclusion zone (centered over the peak) defined by the value of the **Peak exclusion
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92 zone** parameter (see figure). The exclusion zone prevents any secondary peaks from being called on the same strand
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93 within that exclusion zone. In rare cases, it may be desirable to set different exclusion zones upstream (more 5’)
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94 versus downstream (more 3’) of the peak.
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95
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96 .. image:: $PATH_TO_IMAGES/genetrack.png
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97
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98 GeneTrack continues through the data in order of peak height, until no other peaks are found, and in principle will
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99 call a peak at a single isolated tag, if no filter is set using the tool's **Absolute read filter** parameter. A
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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
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101 will be excluded in this case). GeneTrack outputs **chrom** (chromosome number), **strand** (+/W or -/C strand),
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102 **start** (lower coordinate of exclusion zone), **end** (higher coordinate of exclusion zone), and **value** (peak
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103 height). Genetrack's GFF output reports the start (lower coordinate) and end (higher coordinate) of the exclusion
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104 zone.
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105
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106 In principle, the width of the exclusion zone may be as large as the DNA region occupied by the native protein plus
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107 a steric exclusion zone between the protein and the exonuclease. On the other hand the site might be considerably
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108 smaller if the protein is in a denatured state during exonuclease digestion (since it is pre-treated with SDS).
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109
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110 In general, higher resolution data or smaller binding site size data should use smaller sigma values. Large binding
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111 site size data such as 147 bp nucleosomal DNA use a larger sigma value like 20 (-s 20). For transcription factors
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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
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113 varied between ~3 and ~20. Too high of a sigma value may merge two independent nearby binding events. This may be
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114 desirable if closely bound factors are not distinguishable. Too low of a sigma value will cause some tags that
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115 contribute to a binding event to be excluded, because they may not be located sufficiently close to the main peak.
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116 If alternative (mutually exclusive) binding is expected for two overlapping sites, and these sites are to be
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117 independently recorded, then an empirically determined smaller exclusion zone width is set. Thus the value of sigma
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118 is set empirically for each mapped factor, depending upon the resolution and binding site size of the binding event.
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119
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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
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121 only a single coordinate (called Singletons, where stddev=0 in the output file). However, low coverage datasets might
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122 be improved by including them, if additional analysis (e.g., motif discovery) validates them. In addition, idealized
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123 action of the exonuclease in ChIP-exo might place all tags for a peak on a single coordinate.
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124
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125 -----
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126
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127 **Options**
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128
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129 * **Sigma to use when smoothing reads** - Smooths clusters of tags via a Gaussian distribution.
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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.
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131 * **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
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132 * **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
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133 * **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
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134
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135 -----
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136
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137 **Output gff Columns**
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138
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139 1. Chromosome
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140 2. Script
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141 3. Placeholder (no meaning)
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142 4. Start of peak exclusion zone (-e 20)
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143 5. End of peak exclusion zone
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144 6. Tag sum (not peak height or area under curve, which LionDB provides)
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145 7. Strand
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146 8. Placeholder (no meaning)
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147 9. Attributes (standard deviation of reads located within exclusion zone) = fuzziness of peak
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148
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149 -----
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150
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151 **Considerations**
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152
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153 In principle, the width of the exclusion zone may be as large as the DNA region occupied by the native protein
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154 plus a steric exclusion zone between the protein and the exonuclease. On the other hand the site might be considerably
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155 smaller if the protein is in a denatured state during exonuclease digestion (since it is pre-treated with SDS).
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156
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157 In general, higher resolution data or smaller binding site size data should use smaller sigma values. Large binding site
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158 size data such as 147 bp nucleosomal DNA use a larger sigma value like 20 (-s 20). For transcription factors mapped by
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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
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160 between ~3 and ~20. Too high of a sigma value may merge two independent nearby binding events. This may be desirable if
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161 closely bound factors are not distinguishable. Too low of a sigma value will cause some tags that contribute to a binding
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162 event to be excluded, because they may not be located sufficiently close to the main peak. If alternative (mutually
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163 exclusive) binding is expected for two overlapping sites, and these sites are to be independently recorded, then an
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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.
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165
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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
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167 a single coordinate (called Singletons, where stddev=0 in the output file). However, low coverage datasets might be
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168 improved by including them, if additional analysis (e.g., motif discovery) validates them. In addition, idealized action
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169 of the exonuclease in ChIP-exo might place all tags for a peak on a single coordinate.
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170
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171 </help>
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172 <expand macro="citations" />
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173 </tool>