Mercurial > repos > miller-lab > genome_diversity
comparison coverage_distributions.xml @ 12:4b6590dd7250
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| author | miller-lab |
|---|---|
| date | Wed, 12 Sep 2012 17:10:26 -0400 |
| parents | |
| children |
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| 11:d4ec09e8079f | 12:4b6590dd7250 |
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| 1 <tool id="gd_coverage_distributions" name="Coverage" version="1.0.0"> | |
| 2 <description>distributions</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 coverage_distributions.py "$input" "0" "$output" "$output.files_path" | |
| 6 #if $individuals.choice == '0' | |
| 7 "all_individuals" | |
| 8 #else if $individuals.choice == '1' | |
| 9 #set $arg = 'individuals:%s' % str($individuals.p1_input) | |
| 10 "$arg" | |
| 11 #else if $individuals.choice == '2' | |
| 12 #for $population in $individuals.populations | |
| 13 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) | |
| 14 "$arg" | |
| 15 #end for | |
| 16 #end if | |
| 17 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 18 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual) | |
| 19 "$individual_arg" | |
| 20 #end for | |
| 21 </command> | |
| 22 | |
| 23 <inputs> | |
| 24 <param name="input" type="data" format="gd_snp" label="SNP table" /> | |
| 25 | |
| 26 <conditional name="individuals"> | |
| 27 <param name="choice" type="select" label="Individuals"> | |
| 28 <option value="0" selected="true">All</option> | |
| 29 <option value="1">Individuals in a population</option> | |
| 30 <option value="2">Population totals</option> | |
| 31 </param> | |
| 32 <when value="0" /> | |
| 33 <when value="1"> | |
| 34 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> | |
| 35 </when> | |
| 36 <when value="2"> | |
| 37 <repeat name="populations" title="Population" min="1"> | |
| 38 <param name="p_input" type="data" format="gd_indivs" label="individuals" /> | |
| 39 </repeat> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 | |
| 43 <!-- | |
| 44 <param name="data_source" type="select" label="Data source"> | |
| 45 <option value="0" selected="true">Sequence coverage</option> | |
| 46 <option value="1">Genotype quality</option> | |
| 47 </param> | |
| 48 --> | |
| 49 </inputs> | |
| 50 | |
| 51 <outputs> | |
| 52 <data name="output" format="html" /> | |
| 53 </outputs> | |
| 54 | |
| 55 <tests> | |
| 56 <test> | |
| 57 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 58 <param name="choice" value="0" /> | |
| 59 <output name="output" file="test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2"> | |
| 60 <extra_files type="file" name="coverage.pdf" value="test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/> | |
| 61 <extra_files type="file" name="coverage.txt" value="test_out/coverage_distributions/coverage.txt" /> | |
| 62 </output> | |
| 63 </test> | |
| 64 </tests> | |
| 65 | |
| 66 <help> | |
| 67 **What it does** | |
| 68 | |
| 69 This tool reports distributions of SNP reliability indicators for | |
| 70 individuals or populations. The reliability is measured by the sequence | |
| 71 coverage. Textual and graphical reports are generated, where the text | |
| 72 output gives the cumulative distributions. | |
| 73 </help> | |
| 74 </tool> | |
| 75 |