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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>adding your own custom annotations</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">annotate</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11
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12 bgzip -c $annotate_source > tabixed.gz;
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13 tabix -p bed tabixed.gz;
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14
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15 gemini @BINARY@
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16 -f tabixed.gz
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17 -c $column_name
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18 -a $a.a_selector
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19 #if $a.a_selector == 'extract':
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20 -t $a.column_type
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21 -e $a.column_extracts
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22 -o $a.operation
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23 #end if
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24
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25 "${ infile }"
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26 > "${ outfile }"
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27 ]]>
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28
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29 </command>
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30 <expand macro="stdio" />
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31 <inputs>
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2
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32 <expand macro="infile" />
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0
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33 <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
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34
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35 <param name="column_name" size="20" type="text" value=""
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36 label="The name of the column to be added to the variant table" help="(-c)">
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37 <sanitizer invalid_char=" ">
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38 <valid initial="string.letters,string.digits">
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39 <add value="_" />
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40 </valid>
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41 </sanitizer>
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42 </param>
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43 <conditional name="a">
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44 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
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45 <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
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46 <option value="count">How many regions did a variant overlap? (count)</option>
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47 <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option>
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48 </param>
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49 <when value="extract">
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50
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51 <param name="column_extracts" label="Column to extract information from for list annotations"
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52 type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/>
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53
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54
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55 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
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56 help="(-t)">
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57 <option value="float">Decimal precision number (float)</option>
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58 <option value="integer">Integer number (integer)</option>
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59 <option value="text">Text columns such as “valid”, “yes” (text)</option>
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60 </param>
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61
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62 <param name="operation" type="select" label="Operation to apply to the extract column values ..."
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63 help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)">
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64 <option value="mean">Compute the average of the (numeric) values</option>
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65 <option value="median">Compute the median of the (numeric) values</option>
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66 <option value="mix">Compute the minimum of the (numeric) values</option>
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67 <option value="max">Compute the maximum of the (numeric) values</option>
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68 <option value="mode">Compute the maximum of the (numeric) values</option>
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69 <option value="first">Use the value from the first record in the annotation file</option>
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70 <option value="last">Use the value from the last record in the annotation file</option>
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71 <option value="list">Create a comma-separated list of the observed (text) values</option>
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72 <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option>
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73 </param>
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74
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75 </when>
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76 <when value="boolean"/>
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77 <when value="count"/>
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78 </conditional>
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79
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80 </inputs>
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81 <outputs>
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2
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82 <data name="outfile" format="tabular" />
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0
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83 </outputs>
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84 <tests>
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85 <test>
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86 </test>
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87 </tests>
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88 <help>
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89 **What it does**
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90
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91 It is inevitable that researchers will want to enhance the gemini framework with their own, custom annotations. gemini provides a sub-command called annotate for exactly this purpose.
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92
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93 @CITATION@
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94 </help>
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95 <expand macro="citations"/>
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96 </tool>
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