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annotate dpmix.xml @ 19:fa34d259eb8f

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Removed unicode from Fst_ave.c
author miller-lab
date Tue, 23 Oct 2012 14:37:26 -0400
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1 <tool id="gd_dpmix" name="Admixture" version="1.0.0">
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2 <description>: Map genomic intervals resembling specified ancestral populations</description>
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3
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4 <command interpreter="python">
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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"
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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="Dataset">
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14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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15 </param>
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16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
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17 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
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18 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
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19
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20 <param name="data_source" type="select" format="integer" label="Data source">
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21 <option value="0" selected="true">sequence coverage</option>
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22 <option value="1">estimated genotype</option>
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23 </param>
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25 <param name="switch_penalty" type="integer" min="0" value="10" label="Switch penalty" />
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26 </inputs>
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27
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28 <outputs>
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29 <data name="output" format="tabular" />
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30 <data name="output2" format="html" />
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31 </outputs>
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32
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33 <tests>
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34 <test>
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35 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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36 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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37 <param name="ap2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
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38 <param name="p_input" value="test_in/c.gd_indivs" ftype="gd_indivs" />
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39 <param name="data_source" value="0" />
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40 <param name="switch_penalty" value="10" />
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41
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42 <output name="output" file="test_out/dpmix/dpmix.tabular" />
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43
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44 <output name="output2" file="test_out/dpmix/dpmix.html" ftype="html" compare="diff" lines_diff="2">
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45 <extra_files type="file" name="dpmix.pdf" value="test_out/dpmix/dpmix.pdf" compare="sim_size" delta = "10000" />
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46 <extra_files type="file" name="misc.txt" value="test_out/dpmix/misc.txt" />
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47 </output>
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48 </test>
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49 </tests>
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50
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51 <help>
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52
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53 **Dataset formats**
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54
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55 The input datasets are in gd_snp_ and gd_indivs_ formats. It is important for
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56 the Individuals datasets to have unique names and for there to be no overlap
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57 between the two populations. Rename these datasets if
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58 needed to make them unique.
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59 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)
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60
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61 .. _gd_snp: ./static/formatHelp.html#gd_snp
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62 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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63 .. _tabular: ./static/formatHelp.html#tab
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64 .. _Dataset missing?: ./static/formatHelp.html
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65
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66 -----
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67
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68 **What it does**
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69
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70 The user specifies two "ancestral" populations (i.e., sources for
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71 chromosomes) and a set of potentially admixed individuals, and chooses
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72 between the sequence coverage or the estimated genotypes to measure
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73 the similarity of genomic intervals in admixed individuals to the two
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74 classes of ancestral chromosomes. The user also picks a "switch penalty",
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75 typically between 10 and 100. For each potentially admixed individual,
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76 the program divides the genome into three "genotypes": (0) homozygous
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77 for the first ancestral population (i.e., both chromosomes from that
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78 population), (1) heterozygous, or (2) homozygous for the second ancestral
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79 population. Parts of a chromosome that are labeled as "heterochromatic"
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80 are given the non-genotype, 3. Smaller values of the switch penalty
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81 (corresponding to more ancient admixture events) generally lead to the
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82 reconstruction of more frequent changes between genotypes.
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83
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84 There are two output datasets generated. A tabular dataset with chromosome,
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85 start, stop, and pairs of columns containing the "genotypes" from above
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86 and label from the admixed individual. The second dataset is a composite
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87 dataset with general information from the run and a link to a pdf which
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88 graphically shows the ancestral population along each of the chromosomes.
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89 The second link is to a text file with summary information of the
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90 "genotypes" over the whole genome.
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91
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92 </help>
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93 </tool>