Mercurial > repos > miller-lab > genome_diversity
comparison dpmix.xml @ 12:4b6590dd7250
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| author | miller-lab |
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| date | Wed, 12 Sep 2012 17:10:26 -0400 |
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| 11:d4ec09e8079f | 12:4b6590dd7250 |
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| 1 <tool id="gd_dpmix" name="Admixture" version="1.0.0"> | |
| 2 <description>using dynamic programming</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc" | |
| 6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 7 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 8 "$arg" | |
| 9 #end for | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="input" type="data" format="gd_snp" label="Dataset"> | |
| 14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | |
| 15 </param> | |
| 16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> | |
| 17 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> | |
| 18 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> | |
| 19 | |
| 20 <param name="data_source" type="select" format="integer" label="Data source"> | |
| 21 <option value="0" selected="true">sequence coverage</option> | |
| 22 <option value="1">estimated genotype</option> | |
| 23 </param> | |
| 24 | |
| 25 <param name="switch_penalty" type="integer" min="0" value="10" label="Switch penalty" /> | |
| 26 </inputs> | |
| 27 | |
| 28 <outputs> | |
| 29 <data name="output" format="tabular" /> | |
| 30 <data name="output2" format="html" /> | |
| 31 </outputs> | |
| 32 | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 36 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
| 37 <param name="ap2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" /> | |
| 38 <param name="p_input" value="test_in/c.gd_indivs" ftype="gd_indivs" /> | |
| 39 <param name="data_source" value="0" /> | |
| 40 <param name="switch_penalty" value="10" /> | |
| 41 | |
| 42 <output name="output" file="test_out/dpmix/dpmix.tabular" /> | |
| 43 | |
| 44 <output name="output2" file="test_out/dpmix/dpmix.html" ftype="html" compare="diff" lines_diff="2"> | |
| 45 <extra_files type="file" name="dpmix.pdf" value="test_out/dpmix/dpmix.pdf" compare="sim_size" delta = "10000" /> | |
| 46 <extra_files type="file" name="misc.txt" value="test_out/dpmix/misc.txt" /> | |
| 47 </output> | |
| 48 </test> | |
| 49 </tests> | |
| 50 | |
| 51 <help> | |
| 52 **What it does** | |
| 53 | |
| 54 The user specifies two "ancestral" populations (i.e., sources for | |
| 55 chromosomes) and a set of potentially admixed individuals, and chooses | |
| 56 between the sequence coverage or the estimated genotypes to measure | |
| 57 the similarity of genomic intervals in admixed individuals to the two | |
| 58 classes of ancestral chromosomes. The user also picks a "switch penalty", | |
| 59 typically between 10 and 100. For each potentially admixed individual, | |
| 60 the program divides the genome into three "genotypes": (0) homozygous | |
| 61 for the second ancestral population (i.e., both chromosomes from that | |
| 62 population), (1) heterozygous, or (2) homozygous for the second ancestral | |
| 63 population. Parts of a chromosome that are labeled as "heterochromatic" | |
| 64 are given the non-genotype, 3. Smaller values of the switch penalty | |
| 65 (corresponding to more ancient admixture events) generally lead to the | |
| 66 reconstruction of more frequent changes between genotypes. | |
| 67 </help> | |
| 68 </tool> |