Mercurial > repos > miller-lab > genome_diversity
comparison prepare_population_structure.xml @ 12:4b6590dd7250
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| author | miller-lab |
|---|---|
| date | Wed, 12 Sep 2012 17:10:26 -0400 |
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| children |
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| 11:d4ec09e8079f | 12:4b6590dd7250 |
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| 1 <tool id="gd_prepare_population_structure" name="Prepare" version="1.0.0"> | |
| 2 <description>to look for population structure</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path" | |
| 6 #if $individuals.choice == '0' | |
| 7 "all_individuals" | |
| 8 #else if $individuals.choice == '1' | |
| 9 #for $population in $individuals.populations | |
| 10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) | |
| 11 "$pop_arg" | |
| 12 #end for | |
| 13 #end if | |
| 14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual) | |
| 16 "$arg" | |
| 17 #end for | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 <param name="input" type="data" format="gd_snp" label="SNP table" /> | |
| 22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" /> | |
| 23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" /> | |
| 24 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" /> | |
| 25 <conditional name="individuals"> | |
| 26 <param name="choice" type="select" label="Individuals"> | |
| 27 <option value="0" selected="true">All</option> | |
| 28 <option value="1">Choose</option> | |
| 29 </param> | |
| 30 <when value="0" /> | |
| 31 <when value="1"> | |
| 32 <repeat name="populations" title="Population" min="1"> | |
| 33 <param name="p_input" type="data" format="gd_indivs" label="Individuals" /> | |
| 34 </repeat> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data name="output" format="gd_ped"> | |
| 41 <actions> | |
| 42 <action type="metadata" name="base_name" default="admix" /> | |
| 43 </actions> | |
| 44 </data> | |
| 45 </outputs> | |
| 46 | |
| 47 <tests> | |
| 48 <test> | |
| 49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 50 <param name="min_reads" value="3" /> | |
| 51 <param name="min_qual" value="30" /> | |
| 52 <param name="min_spacing" value="0" /> | |
| 53 <param name="choice" value="0" /> | |
| 54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2"> | |
| 55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" /> | |
| 56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" /> | |
| 57 </output> | |
| 58 </test> | |
| 59 </tests> | |
| 60 | |
| 61 <help> | |
| 62 **What it does** | |
| 63 | |
| 64 The tool converts a SNP table into two tables, called "admix.map" and | |
| 65 "admix.ped", needed for estimating the population structure. The user | |
| 66 can read or download those files, or simply pass this tool's output on to | |
| 67 other programs. The user imposes conditions on which SNPs to consider, | |
| 68 such as the minimum coverage and/or quality value for every individual, | |
| 69 or the distance to the closest SNP in the same contig (as named in the | |
| 70 first column of the SNP table). A useful piece of information produced | |
| 71 by the tool is the number of SNPs meeting those conditions, which can | |
| 72 be found by clicking on the "eye" after the program runs. | |
| 73 </help> | |
| 74 </tool> |