Mercurial > repos > miller-lab > genome_diversity
comparison dpmix.xml @ 14:8ae67e9fb6ff
Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:35:56 -0400 |
| parents | |
| children | d6b961721037 |
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| 13:fdb4240fb565 | 14:8ae67e9fb6ff |
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| 1 <tool id="gd_dpmix" name="Admixture" version="1.0.0"> | |
| 2 <description>: Map genomic intervals resembling specified ancestral populations</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 | |
| 53 **Dataset formats** | |
| 54 | |
| 55 The input datasets are in gd_snp_ and gd_indivs_ formats. It is important for | |
| 56 the Individuals datasets to have unique names and for there to be no overlap | |
| 57 between the two populations. Rename these datasets if | |
| 58 needed to make them unique. | |
| 59 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_) | |
| 60 | |
| 61 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
| 62 .. _gd_indivs: ./static/formatHelp.html#gd_indivs | |
| 63 .. _tabular: ./static/formatHelp.html#tab | |
| 64 .. _Dataset missing?: ./static/formatHelp.html | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 **What it does** | |
| 69 | |
| 70 The user specifies two "ancestral" populations (i.e., sources for | |
| 71 chromosomes) and a set of potentially admixed individuals, and chooses | |
| 72 between the sequence coverage or the estimated genotypes to measure | |
| 73 the similarity of genomic intervals in admixed individuals to the two | |
| 74 classes of ancestral chromosomes. The user also picks a "switch penalty", | |
| 75 typically between 10 and 100. For each potentially admixed individual, | |
| 76 the program divides the genome into three "genotypes": (0) homozygous | |
| 77 for the first ancestral population (i.e., both chromosomes from that | |
| 78 population), (1) heterozygous, or (2) homozygous for the second ancestral | |
| 79 population. Parts of a chromosome that are labeled as "heterochromatic" | |
| 80 are given the non-genotype, 3. Smaller values of the switch penalty | |
| 81 (corresponding to more ancient admixture events) generally lead to the | |
| 82 reconstruction of more frequent changes between genotypes. | |
| 83 | |
| 84 There are two output datasets generated. A tabular dataset with chromosome, | |
| 85 start, stop, and pairs of columns containing the "genotypes" from above | |
| 86 and label from the admixed individual. The second dataset is a composite | |
| 87 dataset with general information from the run and a link to a pdf which | |
| 88 graphically shows the ancestral population along each of the chromosomes. | |
| 89 The second link is to a text file with summary information of the | |
| 90 "genotypes" over the whole genome. | |
| 91 | |
| 92 </help> | |
| 93 </tool> |