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1 <tool id="gd_filter_gd_snp" name="Filter SNPs" version="1.0.0">
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2 <description>: Discard some SNPs based on coverage or quality</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" "$output" "$lo_coverage" "$hi_coverage" "$low_ind_cov" "$lo_quality"
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6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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7 #set $arg = '%s:%s' % ($individual_col, $individual)
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8 "$arg"
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9 #end for
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10 </command>
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11
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12 <inputs>
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13 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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14 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
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15 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" />
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16 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" />
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17 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" />
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18 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" />
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19 </inputs>
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20
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21 <outputs>
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22 <data name="output" format="gd_snp" metadata_source="input" />
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23 </outputs>
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24
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25 <tests>
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26 <test>
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27 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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28 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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29 <param name="choice" value="1" />
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30 <param name="lo_coverage" value="0" />
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31 <param name="hi_coverage" value="1000" />
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32 <param name="low_ind_cov" value="3" />
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33 <param name="lo_quality" value="30" />
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34 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
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35 </test>
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36 </tests>
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37
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38 <help>
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39
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40 **Dataset formats**
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41
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42 The input datasets are in gd_snp_ and gd_indivs_ formats.
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43 The output dataset is in gd_snp_ format. (`Dataset missing?`_)
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44
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45 .. _gd_snp: ./static/formatHelp.html#gd_snp
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46 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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47 .. _Dataset missing?: ./static/formatHelp.html
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48
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49 -----
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50
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51 **What it does**
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52
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53 The user specifies that some of the individuals in a gd_snp dataset form a
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54 "population", by supplying a list that has been previously created using the
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55 Specify Individuals tool. SNPs are then discarded if their total coverage
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56 for the population is too low or too high, or if their coverage or quality
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57 score for any individual in the population is too low.
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58
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59 -----
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60
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61 **Example**
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62
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63 - input gd_snp::
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64
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65 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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66 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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67 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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68 etc.
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69
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70 - input individuals::
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71
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72 9 PB1
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73 13 PB2
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74 17 PB3
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75
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76 - output when the lower bound on individual coverage is "3"::
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77
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78 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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79 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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80 etc.
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81
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82 </help>
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83 </tool>
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