Mercurial > repos > miller-lab > genome_diversity
comparison dpmix.xml @ 24:248b06e86022
Added gd_genotype datatype. Modified tools to support new datatype.
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 28 May 2013 16:24:19 -0400 |
| parents | d6b961721037 |
| children | cba0d7a63b82 |
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| 23:66a183c44dd5 | 24:248b06e86022 |
|---|---|
| 1 <tool id="gd_dpmix" name="Admixture" version="1.0.0"> | 1 <tool id="gd_dpmix" name="Admixture" version="1.1.0"> |
| 2 <description>: Map genomic intervals resembling specified ancestral populations</description> | 2 <description>: Map genomic intervals resembling specified ancestral populations</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 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" | 5 dpmix.py "$input" |
| 6 #if $input_type.choice == '0' | |
| 7 "gd_snp" "$input_type.data_source" | |
| 8 #else if $input_type.choice == '1' | |
| 9 "gd_genotype" "1" | |
| 10 #end if | |
| 11 "$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) | 12 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) |
| 7 #set $arg = '%s:%s' % ($individual_col, $individual) | 13 #set $arg = '%s:%s' % ($individual_col, $individual) |
| 8 "$arg" | 14 "$arg" |
| 9 #end for | 15 #end for |
| 10 </command> | 16 </command> |
| 11 | 17 |
| 12 <inputs> | 18 <inputs> |
| 13 <param name="input" type="data" format="gd_snp" label="SNP dataset"> | 19 <conditional name="input_type"> |
| 14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | 20 <param name="choice" type="select" format="integer" label="Input format"> |
| 15 </param> | 21 <option value="0" selected="true">gd_snp</option> |
| 22 <option value="1">gd_genotype</option> | |
| 23 </param> | |
| 24 <when value="0"> | |
| 25 <param name="input" type="data" format="gd_snp" label="SNP dataset"> | |
| 26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | |
| 27 </param> | |
| 28 | |
| 29 <param name="data_source" type="select" format="integer" label="Similarity metric"> | |
| 30 <option value="0">sequence coverage</option> | |
| 31 <option value="1" selected="true">estimated genotype</option> | |
| 32 </param> | |
| 33 </when> | |
| 34 <when value="1"> | |
| 35 <param name="input" type="data" format="gd_genotype" label="Genotype dataset"> | |
| 36 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | |
| 37 </param> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 | |
| 16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> | 41 <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" /> | 42 <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" /> | 43 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> |
| 19 | |
| 20 <param name="data_source" type="select" format="integer" label="Similarity metric"> | |
| 21 <option value="0" selected="true">sequence coverage</option> | |
| 22 <option value="1">estimated genotype</option> | |
| 23 </param> | |
| 24 | 44 |
| 25 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> | 45 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> |
| 26 </inputs> | 46 </inputs> |
| 27 | 47 |
| 28 <outputs> | 48 <outputs> |
| 50 | 70 |
| 51 <help> | 71 <help> |
| 52 | 72 |
| 53 **Dataset formats** | 73 **Dataset formats** |
| 54 | 74 |
| 55 The input datasets are in gd_snp_ and gd_indivs_ formats. It is important for | 75 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. It is important for |
| 56 the Individuals datasets to have unique names and for there to be no overlap | 76 the Individuals datasets to have unique names and for there to be no overlap |
| 57 between the two populations. Rename these datasets if | 77 between the two populations. Rename these datasets if |
| 58 needed to make them unique. | 78 needed to make them unique. |
| 59 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_) | 79 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_) |
| 60 | 80 |
| 61 .. _gd_snp: ./static/formatHelp.html#gd_snp | 81 .. _gd_snp: ./static/formatHelp.html#gd_snp |
| 82 .. _gd_genotype: ./static/formatHelp.html#gd_genotype | |
| 62 .. _gd_indivs: ./static/formatHelp.html#gd_indivs | 83 .. _gd_indivs: ./static/formatHelp.html#gd_indivs |
| 63 .. _tabular: ./static/formatHelp.html#tab | 84 .. _tabular: ./static/formatHelp.html#tab |
| 64 .. _Dataset missing?: ./static/formatHelp.html | 85 .. _Dataset missing?: ./static/formatHelp.html |
| 65 | 86 |
| 66 ----- | 87 ----- |