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1 <tool id="gd_coverage_distributions" name="Coverage" version="1.0.0">
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2 <description>distributions</description>
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3
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4 <command interpreter="python">
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5 coverage_distributions.py "$input" "0" "$output" "$output.extra_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 #set $arg = 'individuals:%s' % str($individuals.p1_input)
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10 "$arg"
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11 #else if $individuals.choice == '2'
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12 #for $population in $individuals.populations
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13 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
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14 "$arg"
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15 #end for
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16 #end if
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17 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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18 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
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19 "$individual_arg"
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20 #end for
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21 </command>
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22
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23 <inputs>
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24 <param name="input" type="data" format="wsf" label="SNP table" />
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25
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26 <conditional name="individuals">
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27 <param name="choice" type="select" label="Individuals">
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28 <option value="0" selected="true">All</option>
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29 <option value="1">Individuals in a population</option>
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30 <option value="2">Population totals</option>
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31 </param>
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32 <when value="0" />
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33 <when value="1">
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34 <param name="p1_input" type="data" format="ind" label="Population individuals" />
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35 </when>
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36 <when value="2">
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37 <repeat name="populations" title="Population" min="1">
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38 <param name="p_input" type="data" format="ind" label="individuals" />
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39 </repeat>
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40 </when>
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41 </conditional>
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42
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43 <!--
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44 <param name="data_source" type="select" label="Data source">
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45 <option value="0" selected="true">Sequence coverage</option>
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46 <option value="1">Genotype quality</option>
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47 </param>
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48 -->
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49 </inputs>
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50
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51 <outputs>
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52 <data name="output" format="html" />
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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58 <param name="choice" value="0" />
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59 <output name="output" file="genome_diversity/test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2">
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60 <extra_files type="file" name="coverage.pdf" value="genome_diversity/test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/>
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61 <extra_files type="file" name="coverage.txt" value="genome_diversity/test_out/coverage_distributions/coverage.txt" />
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62 </output>
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63 </test>
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64 </tests>
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65
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66 <help>
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67 **What it does**
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68
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69 This tool reports distributions of SNP reliability indicators for
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70 individuals or populations. The reliability is measured by the sequence
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71 coverage. Textual and graphical reports are generated, where the text
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72 output gives the cumulative distributions.
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73 </help>
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74 </tool>
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75
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