Mercurial > repos > miller-lab > genome_diversity
comparison dpmix.xml @ 31:a631c2f6d913
Update to Miller Lab devshed revision 3c4110ffacc3
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Fri, 20 Sep 2013 13:25:27 -0400 |
| parents | 4188853b940b |
| children |
comparison
equal
deleted
inserted
replaced
| 30:4188853b940b | 31:a631c2f6d913 |
|---|---|
| 1 <tool id="gd_dpmix" name="Admixture" version="1.1.0"> | 1 <tool id="gd_dpmix" name="Admixture" version="1.2.0"> |
| 2 <description>: Map genomic intervals resembling specified source populations</description> | 2 <description>: Map genomic intervals resembling specified source populations</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 #import json | 5 #import json |
| 6 #import base64 | 6 #import base64 |
| 29 #else if $user_het.choice == '1' | 29 #else if $user_het.choice == '1' |
| 30 #set $het_arg = $user_het.het_file | 30 #set $het_arg = $user_het.het_file |
| 31 #else if $user_het.choice == '2' | 31 #else if $user_het.choice == '2' |
| 32 #set $het_arg = 'use_none' | 32 #set $het_arg = 'use_none' |
| 33 #end if | 33 #end if |
| 34 '$switch_penalty' '$ap1_input' '$ap1_input.name' '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '1' | 34 '$switch_penalty' |
| 35 #if $use_reference.choice == '0' | |
| 36 '$ap1_input' '$ap1_input.name' | |
| 37 #else if $use_reference.choice == '1' | |
| 38 '/dev/null' 'reference' | |
| 39 #end if | |
| 40 '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '$add_logs' | |
| 35 </command> | 41 </command> |
| 36 | 42 |
| 37 <inputs> | 43 <inputs> |
| 38 <conditional name="input_type"> | 44 <conditional name="input_type"> |
| 39 <param name="choice" type="select" format="integer" label="Input format"> | 45 <param name="choice" type="select" format="integer" label="Input format"> |
| 55 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> | 61 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> |
| 56 </param> | 62 </param> |
| 57 </when> | 63 </when> |
| 58 </conditional> | 64 </conditional> |
| 59 | 65 |
| 60 <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" /> | 66 <conditional name="use_reference"> |
| 67 <param name="choice" type="select" format="integer" label="History item or Reference sequence"> | |
| 68 <option value="0" selected="true">History item</option> | |
| 69 <option value="1">Reference sequence</option> | |
| 70 </param> | |
| 71 <when value="0"> | |
| 72 <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" /> | |
| 73 </when> | |
| 74 <when value="1" /> | |
| 75 </conditional> | |
| 76 | |
| 61 <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" /> | 77 <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" /> |
| 62 | 78 |
| 63 <conditional name="third_pop"> | 79 <conditional name="third_pop"> |
| 64 <param name="choice" type="select" format="integer" label="Include third source population"> | 80 <param name="choice" type="select" format="integer" label="Include third source population"> |
| 65 <option value="0" selected="true">no</option> | 81 <option value="0" selected="true">no</option> |
| 85 <when value="1"> | 101 <when value="1"> |
| 86 <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" /> | 102 <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" /> |
| 87 </when> | 103 </when> |
| 88 </conditional> | 104 </conditional> |
| 89 | 105 |
| 90 <!-- | |
| 91 <param name="add_logs" type="select" format="integer" label="Probabilities"> | 106 <param name="add_logs" type="select" format="integer" label="Probabilities"> |
| 92 <option value="1" selected="true">add logs of probabilities</option> | 107 <option value="1" selected="true">add logs of probabilities</option> |
| 93 <option value="0">add probabilities</option> | 108 <option value="0">add probabilities</option> |
| 94 </param> | 109 </param> |
| 95 --> | |
| 96 | 110 |
| 97 </inputs> | 111 </inputs> |
| 98 | 112 |
| 99 <outputs> | 113 <outputs> |
| 100 <data name="output" format="tabular" /> | 114 <data name="output" format="tabular" /> |
| 101 <data name="output2" format="html" /> | 115 <data name="output2" format="html" /> |
| 102 </outputs> | 116 </outputs> |
| 117 | |
| 118 <requirements> | |
| 119 <requirement type="package" version="0.1">gd_c_tools</requirement> | |
| 120 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
| 121 </requirements> | |
| 103 | 122 |
| 104 <tests> | 123 <tests> |
| 105 <test> | 124 <test> |
| 106 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | 125 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> |
| 107 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | 126 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> |