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1 <tool id="gd_specify" name="Specify Individuals" version="1.0.0">
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2 <description>: Define a collection of individuals from a gd_snp dataset</description>
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3
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4 <command interpreter="bash">
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5 echo.bash "$input" "$output"
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6 #for $individual in str($individuals).split(',')
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7 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
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8 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
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9 #set $arg = '\t'.join([$individual_col, $individual, ''])
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10 "$arg"
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11 #end for
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12 </command>
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13
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14 <inputs>
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15 <param name="input" type="data" format="gd_snp" label="SNP dataset"/>
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16 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
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17 <options>
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18 <filter type="data_meta" ref="input" key="individual_names" />
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19 </options>
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20 <validator type="no_options" message="You must select at least one individual."/>
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21 </param>
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22 <param name="outname" type="text" size="20" label="Label for this collection">
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23 <validator type="empty_field" message="You must enter a label."/>
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24 #used to be "Individuals from ${input.hid}"
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25 </param>
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26 </inputs>
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27
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28 <outputs>
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29 <data name="output" format="gd_indivs" label="${outname}" />
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30 </outputs>
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31
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32 <tests>
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33 <test>
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34 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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35 <param name="individuals" value="PB1,PB2" />
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36 <output name="output" file="test_in/a.gd_indivs" />
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37 </test>
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38 </tests>
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39
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40 <help>
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41
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42 **Dataset formats**
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43
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44 The input dataset is in gd_snp_ format;
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45 the output is in gd_indivs_ format. (`Dataset missing?`_)
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46
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47 .. _gd_snp: ./static/formatHelp.html#gd_snp
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48 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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49 .. _Dataset missing?: ./static/formatHelp.html
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50
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51 -----
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52
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53 **What it does**
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54
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55 This tool makes a list of selected entities (the sets of four columns
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56 representing individuals or groups) from a gd_snp dataset. It does not copy
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57 the SNP data; it just records which entities should be considered as belonging
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58 to some collection or population. The label you specify is used to name the
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59 output dataset in your history. This list can then be used to instruct other
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60 tools to work on just part of the original gd_snp dataset.
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61
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62 -----
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63
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64 **Example**
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65
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66 - input::
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67
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68 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
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69 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
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70 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
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71 etc.
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72
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73 - input metadata::
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74
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75 #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc",
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76 #"1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q",
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77 #"pair","dist","prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],
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78 #"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
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79
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80 - output when individuals PB1, PB2, and PB3 are selected::
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81
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82 9 PB1
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83 13 PB2
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84 17 PB3
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85
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86 </help>
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87 </tool>
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