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1 <tool id="gd_prepare_population_structure" name="Prepare" version="1.0.0">
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2 <description>to look for population structure</description>
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3
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4 <command interpreter="python">
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5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
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6 #if $individuals.choice == '0'
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7 "all_individuals"
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8 #else if $individuals.choice == '1'
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9 #for $population in $individuals.populations
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10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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11 "$pop_arg"
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12 #end for
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13 #end if
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14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
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16 "$arg"
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17 #end for
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18 </command>
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19
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20 <inputs>
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21 <param name="input" type="data" format="wsf" label="SNP table" />
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22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
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23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
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24 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
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25 <conditional name="individuals">
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26 <param name="choice" type="select" label="Individuals">
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27 <option value="0" selected="true">All</option>
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28 <option value="1">Choose</option>
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29 </param>
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30 <when value="0" />
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31 <when value="1">
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32 <repeat name="populations" title="Population" min="1">
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33 <param name="p_input" type="data" format="ind" label="Individuals" />
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34 </repeat>
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35 </when>
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="output" format="wped">
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41 <actions>
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42 <action type="metadata" name="base_name" default="admix" />
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43 </actions>
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44 </data>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="input" value="test_in/sample.wsf" ftype="wsf" />
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50 <param name="min_reads" value="3" />
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51 <param name="min_qual" value="30" />
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52 <param name="min_spacing" value="0" />
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53 <param name="choice" value="0" />
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54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
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55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
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56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
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57 </output>
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58 </test>
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59 </tests>
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60
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61 <help>
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62 **What it does**
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63
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64 The tool converts a SNP table into two tables, called "admix.map" and
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65 "admix.ped", needed for estimating the population structure. The user
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66 can read or download those files, or simply pass this tool's output on to
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67 other programs. The user imposes conditions on which SNPs to consider,
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68 such as the minimum coverage and/or quality value for every individual,
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69 or the distance to the closest SNP in the same contig (as named in the
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70 first column of the SNP table). A useful piece of information produced
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71 by the tool is the number of SNPs meeting those conditions, which can
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72 be found by clicking on the "eye" after the program runs.
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73 </help>
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74 </tool>
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