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1 <tool id="gd_modify_snp_table" name="Modify" version="1.0.0">
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2 <description>a SNP table</description>
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3
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4 <command interpreter="python">
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5 modify_snp_table.py "$input" "$p1_input" "$output"
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6 #if $limit_coverage.choice == "0"
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7 "-1" "-1" "-1" "-1"
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8 #else
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9 "${limit_coverage.lo_coverage}" "${limit_coverage.hi_coverage}" "${limit_coverage.low_ind_cov}" "${limit_coverage.lo_quality}"
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10 #end if
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11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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12 #set $arg = '%s:%s' % ($individual_col, $individual)
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13 "$arg"
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14 #end for
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15 </command>
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16
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17 <inputs>
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18 <param name="input" type="data" format="wsf" label="SNP table" />
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19 <param name="p1_input" type="data" format="ind" label="Population individuals" />
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20 <conditional name="limit_coverage">
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21 <param name="choice" type="select" format="integer" label="Option">
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22 <option value="0" selected="true">add columns to the SNP table</option>
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23 <option value="1">discard some SNPs</option>
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24 </param>
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25 <when value="0" />
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26 <when value="1">
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27 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" />
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28 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" />
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29 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" />
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30 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" />
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31 </when>
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32 </conditional>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="output" format="wsf" metadata_source="input" />
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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42 <param name="p1_input" value="genome_diversity/test_in/a.ind" ftype="ind" />
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43 <param name="choice" value="1" />
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44 <param name="lo_coverage" value="0" />
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45 <param name="hi_coverage" value="1000" />
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46 <param name="low_ind_cov" value="3" />
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47 <param name="lo_quality" value="30" />
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48 <output name="output" file="genome_diversity/test_out/modify_snp_table/modify.wsf" />
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49 </test>
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50 </tests>
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51
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52 <help>
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53 **What it does**
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54
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55 The user specifies that some of the individuals in the selected SNP table are
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56 form a "population" that has been previously defined using the Galaxy tool to
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57 select individuals from a SNP table. One option is for the program to append
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58 four columns to the table, giving the total counts for the two alleles, the
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59 "genotype" for the population and the maximum quality value, taken over all
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60 individuals in the population. If all defined genotypes in the population
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61 are 2 (agree with the reference), the population's genotype is 2; similarly
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62 for 0; otherwise the genotype is 1 (unless all individuals have undefined
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63 genotype, in which case it is -1. The other option is to remove rows from
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64 the table for which the total coverage for the population is either too low
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65 or too high, and/or if the individual coverage or quality value is too low.
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66 </help>
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67 </tool>
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