Mercurial > repos > iuc > genehunter_modscore

annotate genehunter_modscore.xml @ 0:9e6a43112688 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
author iuc
date Sat, 09 Dec 2017 05:58:25 -0500
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9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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1 <tool id="genehunter_modscore" name="Genehunter-Modscore" version="@VERSION@.0" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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2 <description>Linkage and Haplotypes analysis</description>
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3 <macros>
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4 <token name="@VERSION@">3.0.0</token>
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5 <xml name="macro_npl_opts" >
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6 <param name="extra_npl_score" type="select" label="Type of NPL scoring">
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7 <option value="all" selected="true" >All</option>
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8 <option value="pairs" >Pairs</option>
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9 <option value="hom" >Homozygous</option>
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10 </param>
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11 </xml>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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12 <!-- Input test file collection -->
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13 <xml name="test_input_files">
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14 <param name="inp_ped" value="pedin_1.21" />
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15 <param name="inp_dat" value="datain_1.21" />
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16 <param name="inp_map" value="map_1.21" />
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17 </xml>
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18 <!-- End Input test file collection -->
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19 <!-- Output test file(s) -->
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20 <xml name="test_output_fparam">
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21 <output name="fparam" >
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22 <assert_contents>
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23 <has_text_matching expression="\s*\d+\.\d+\s+-\d+\.\d+(\s+\d+\.\d+){2}\s+rs17000204$" />
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24 </assert_contents>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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25 </output>
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26 </xml>
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27 <xml name="test_output_haplo">
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28 <output name="ihaplo" >
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29 <assert_contents>
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30 <has_text_matching expression="1\s+206006\s+206001\s+206002\s+2\s+2(\s+[0-2])+" />
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31 </assert_contents>
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32 </output>
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33 </xml>
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34 <!-- End Output test file(s) -->
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35 </macros>
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36 <requirements>
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37 <requirement type="package" version="@VERSION@" >ghm</requirement>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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38 <requirement type="package" version="2017.3" >linkage2allegro</requirement>
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39 </requirements>
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40 <version_command><![CDATA[
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41 echo q | ghm | grep -oP "(?<=(\(version\ ))[^)]+"
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42 ]]>
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43 </version_command>
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44 <command detect_errors='exit_code'><![CDATA[
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45 ghm < '$setup_file'
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46
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47 && linkage2allegro
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48 '${inp_ped}'
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49 '${inp_map}'
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50 genehunter
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51 -l gh.out
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52 #if $section_haplo.analysis_haplo.extra_haplotype
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53 -h haplo.dump
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54 #end if
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55
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56 && mv linkage.allegro_lod '${fparam}'
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57 #if $section_haplo.analysis_haplo.extra_haplotype
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58 && mv linkage.allegro_haplo '${ihaplo}'
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59 #end if
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60 ]]>
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61 </command>
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62 <configfiles>
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63 <configfile name="setup_file" ><![CDATA[
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64 photo gh.out
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65
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66 ps off
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67
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68 ## Initiate mod score lod calculation and store IVs, off by default
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69 modcalc ${section_options.section_pvalues.advanced_options_modcalc.extra_modcalc}
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70 ## global / single / off
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71
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72 haplotype ${section_haplo.analysis_haplo.extra_haplotype}
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73 ## on / off, generate Haplotypes
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74
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75 #if $section_haplo.analysis_haplo.extra_haplotype
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76 haplotype method ${section_haplo.analysis_haplo.extra_haplotype_method}
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77 ## [MaxProb] / Viterbi
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78 #end if
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79
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80 analysis ${section_linkage.npl_scoring.extra_mod_analysis}
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81 ## NPL / LOD / BOTH, type of linkage analysis
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82
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83 #if $section_linkage.npl_scoring.extra_mod_analysis.value != 'LOD':
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84 score ${section_linkage.npl_scoring.extra_npl_score}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
85 ## pairs / all / hom
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
86 #else
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
87 score all
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
88 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
89
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
90 #if $section_linkage.extra_singlepoint
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
91 single point ${section_linkage.extra_singlepoint}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
92 ## on / off, dont use multi-point parametric
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
93 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
94
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
95 ## -- Re-enable in 3.1
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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96 ## Algebraic calculation for P-values, default on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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97 ## #if $section_options.section_pvalues.advanced_options_alg.extra_alg
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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98 ## alg ${section_options.section_pvalues.advanced_options_alg.extra_alg}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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99 ## Use more memory for algebraic calculations
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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100 ## algebra ${section_options.section_pvalues.advanced_options_alg.extra_alg_mem}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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101 ## #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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102
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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103 ## Add custom trait models
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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104 #if $section_options.section_pvalues.advanced_options_model.extra_mod_model
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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105 model ${section_options.section_pvalues.advanced_options_model.extra_mod_modeldisfreq} ${section_options.section_pvalues.advanced_options_model.extra_mod_modelpenet}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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106 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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107
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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108 ## Range of markers positions instead of all range
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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109 #if $section_options.section_range.advanced_options_positions.extra_mod_positions
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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110 ## #try
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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111 ## #assert $section_options.section_range.advanced_options_positions.extra_mod_positions_lowest < $section_options.section_range.advanced_options_positions.extra_mod_positions_highest
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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112 ## #except AssertionError
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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113 ## #echo Range minimum is not less than the maximum
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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114 ## #end try
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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115 positions ${section_options.section_range.advanced_options_positions.extra_mod_positions_lowest} ${section_options.section_range.advanced_options_positions.extra_mod_positions_highest}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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116 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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117
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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118 ## Untyped, default on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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119 #if $section_haplo.analysis_haplo.extra_haplotype or $section_options.section_sample.extra_includeuntyped
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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120 include untyped on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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121 #else:
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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122 include untyped off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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123 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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124
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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125 ## Eliminate uninformative individuals, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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126 discard ${section_options.section_sample.extra_discard}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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127
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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128 ## Use untyped founders, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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129 ufo ${section_options.section_sample.extra_ufo}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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130
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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131 ## Restrict penetrances so that hom wildtype LEQ het LEQ hom mutant, on default
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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132 pr ${section_options.section_allfreq.extra_mod_penetrancerestrict}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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133
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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134 ## Restrict disease allele frequency to be not higher than the highest allfreq (default 0.5)
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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135 #if $section_options.section_allfreq.extra_mod_allfreq
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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136 ar $section_options.section_allfreq.extra_mod_allfreq
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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137 ## Set upper disease allele freq for MOD, default 0.5 ( 0 -> 1 )
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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138 ha $section_options.section_allfreq.extra_mod_highallele
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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diff changeset
139 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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140
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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141 ## Number of parameters varied together in MOD, default 2 ( 1 -> 5 )
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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142 dimensions ${section_options.section_pvalues.extra_mod_dimensions}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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143
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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144 ## Normalize Allele Frequencies, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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145 naf ${section_options.section_allfreq.extra_nmaf}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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146
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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147 ## off by default
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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148 #if '${section_options.section_pvalues.advanced_options_modcalc.extra_modcalc}' == 'single':
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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149 ## Number of trait models saved in MOD score.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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150 ## Only works if algebraic calc is off, and in single modcalc
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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151 #if not('${extra_alg}'):
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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152 #if '${extra_mod_savedmodels}'!=-1:
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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153 saved models $extra_mod_savedmodels
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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154 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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parents:
diff changeset
155 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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156
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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157 ## Long output for modcalc single
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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158 $section_options.section_pvalues.extra_mod_longmod
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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159
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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160 ## Calculate P-values only at the best position, off by default
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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diff changeset
161 $section_options.section_pvalues.extra_mod_bep
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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diff changeset
162 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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163
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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164
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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165 ## Calculate p-values for MOD/LOD scores
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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166 #if $section_options.section_pvalues.advanced_options_calcpval.extra_calcpval
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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167 cpv $section_options.section_pvalues.advanced_options_calcpval.extra_calcpval_file
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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168 ## Number of replicates in P-score evaluation, default 0
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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169 #if $section_options.section_pvalues.advanced_options_calcpval.extra_cpv_nor > 0
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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170 nor $section_options.section_pvalues.advanced_options_calcpval.extra_cpv_nor
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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171 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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172 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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173
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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174 ## Number of sequential simulations in P-score evaluation, default 0
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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175 seq ${section_options.section_pvalues.extra_seq}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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176
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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177 ## Store replicates during P-score evaluation, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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178 str ${section_options.section_pvalues.extra_storereplicates} ## pre / both / off (default)
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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179
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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180 ## Simulate untyped individuals, required for haplotypes
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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181 #if $section_haplo.analysis_haplo.extra_haplotype or $section_options.section_sample.extra_sun
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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182 sun on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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183 #else
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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184 sun off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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185 #end if
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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186
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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187 ## Set random seed for P-score evaluation, default -1
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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188 srs ${section_options.section_pvalues.extra_srs}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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189
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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190 ## Display distribution of replicates, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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191 sdi ${section_options.section_display.extra_sdi}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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192
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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193 #### General
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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194 ## Count the number of recombintions, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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195 count recs ${section_options.section_display.extra_countrec}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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196
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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197 ## Do not skip fully homozygous markers when generating haplotypes, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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198 fin ${section_options.section_sample.extra_cpv_fin}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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199
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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200 ## Print scores to screen, default on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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201 display scores on
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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202
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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203 ## Margin before and after marker range to compute scores, default 0 cM
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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204 off end ${section_options.section_range.extra_offend}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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205
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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206 ## Distance between adjacent scores, either in cM 'distance' irrespective of
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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207 ## map, or equal 'steps'. Default steps 2
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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208 increment ${section_options.section_range.advanced_options_increment.extra_increment_type} ${section_options.section_range.advanced_options_increment.extra_increment_sizepavu}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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209
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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210 ## Units, default haldane
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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211 map function ${section_options.section_display.extra_mapfunc}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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212 ## Units in scan output, default cM
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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213 units ${section_options.section_display.extra_scan_units}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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214
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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215 ## Max pedigree size calculated by 2N - F, default 19, trim individuals beyond this
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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216 max bits ${section_options.section_range.extra_maxbits}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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217 ## Split pedigree larger than max ped size, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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218 skip large ${section_options.section_range.extra_maxbits_skiplarge}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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219 ## Stores IBD matrics for linkage, default off
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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220 cs ${section_options.section_pvalues.extra_computesharing}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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221
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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222
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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223 load markers ${inp_dat}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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224 read map ${inp_map}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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225 use
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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226
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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227 scan ${inp_ped}
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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228
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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229 ## Show total scores from a scan of multiple peds
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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230 ## - 'het' [alpha], if not given then alpha varies
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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231 ## - 'stat'
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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232 ## default below, overridden by params
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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233 total stat het
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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234
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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235
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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236 ## TODO:
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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237 ## Qualitative / Quantitative trait mapping of sibs, Variance component analysis, TDT
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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238 q
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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239 ]]>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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240 </configfile>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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241 </configfiles>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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242 <inputs>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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243 <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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244 <param name="inp_dat" type="data" format="linkage_datain" label="Recombination Freqs" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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245 <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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246
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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247 <section name="section_haplo" title="Haplotypes" expanded="true" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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248 <conditional name="analysis_haplo" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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249 <param name="extra_haplotype" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Haplotype Analysis" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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250 <when value="on">
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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251 <param name="extra_haplotype_method" type="select" label="Haplotype Reconstruction Algorithm. MaxProb is fastest, and has more global solution." >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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252 <option value="MaxProb" selected="true" >Maximisation Probability</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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253 <option value="Viterbi" >Viterbi</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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254 </param>
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255 </when>
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256 <when value="off" />
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257 </conditional>
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258 </section>
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259
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iuc
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260 <section name="section_linkage" title="Linkage" expanded="false" >
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261 <param name="extra_singlepoint" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Single-point Analysis"/>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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262 <conditional name="npl_scoring" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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263 <param name="extra_mod_analysis" type="select" label="Type of linkage analysis" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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264 <option value="BOTH" selected="true" >Both</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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265 <option value="NPL" >Non-paremetric Linkage</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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266 <option value="LOD" >Logarithm-of-the-Odds</option>
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267 </param>
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iuc
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268 <when value="BOTH" ><expand macro="macro_npl_opts" /></when>
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iuc
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269 <when value="NPL" ><expand macro="macro_npl_opts" /></when>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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270 <when value="LOD" />
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271 </conditional>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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272 </section>
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273
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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274 <section name="section_options" expanded="false" title="Advanced Options" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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275 <!-- P-values -->
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276 <section name="section_pvalues" expanded="false"
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277 title="P-value Options" >
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278 <conditional name="advanced_options_alg" >
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279 <param name="extra_alg" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use Algebraic calculations for P-Values"/>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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280
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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281 <when value="on" >
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282 <param name="extra_alg_mem" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Remove large memory restrictions for algebraic calculations" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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283 </when>
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284 <when value="off" >
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285 <param name="extra_mod_savedmodels" type="integer" value="-1" label="Number of models to save" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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286 </when>
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287 </conditional>
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288
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289 <conditional name="advanced_options_model" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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290 <param name="extra_mod_model" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use custom trait models" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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291 <when value="on" >
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292 <param name="extra_mod_modeldisfreq" type="float" value="" min="0" max="1" label="Disease allele frequency" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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293 <param name="extra_mod_modelpenet" type="text" value="" label="3 or 4 penetrances" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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294 </when>
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295 <when value="off" />
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296 </conditional>
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297
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298 <conditional name="advanced_options_calcpval" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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299 <param name="extra_calcpval" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Calculate P-values for MOD/LOD scores" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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300
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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301 <when value="on" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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302 <param name="extra_calcpval_file" type="data" format="txt" label="Filename to produce values" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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303 <param name="extra_cpv_nor" type="integer" value="0" min="0" label="Number of replicates in P-value calculations" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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304 </when>
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iuc
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305 <when value="off" />
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306 </conditional>
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307
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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308 <conditional name="advanced_options_modcalc" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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309 <param name="extra_modcalc" type="select" label="Inheritance Vector storage for LOD and P-value calculations" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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310 <option value="global" >Global</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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311 <option value="single" >Single</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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312 <option value="off" selected="true" >Off</option>
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313 </param>
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314 <when value="single" >
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315 <param name="extra_mod_longmod" type="boolean" truevalue="lm on" falsevalue="" checked="false" label="Produce long output for scores" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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316 <param name="extra_mod_bep" type="boolean" truevalue="bep on" falsevalue="" checked="false" label="Calculate P-values only at the best LOD positions" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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317 </when>
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318 <when value="global" />
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319 <when value="off" />
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320 </conditional>
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321
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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322 <param name="extra_seq" type="integer" value="0" min="0" label="Number of sequential simulations in P-value calculations" />
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323 <param name="extra_storereplicates" type="select" label="Store replicates during P-value calculations" >
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324 <option value="pre" >Pre</option>
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325 <option value="both" >Both</option>
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326 <option value="off" selected="true" >Off</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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327 </param>
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328 <param name="extra_srs" type="integer" value="-1" label="Set Random seed for P-value calculations" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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329 <param name="extra_computesharing" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Store IBD matrices" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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330 <param name="extra_mod_dimensions" type="integer" min="1" max="5" value="2" label="Number of parameters to vary in LOD calculations" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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331 </section>
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332 <!-- End of P Values: Works -->
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333
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334 <!-- Display Options -->
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335 <section name="section_display" expanded="false" title="Display options" >
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336 <param name="extra_sdi" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Display distribution of replicates" />
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iuc
parents:
diff changeset
337 <param name="extra_countrec" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Print the number of recombinations" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
338 <param name="extra_mapfunc" type="select" label="Genetic map function units" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
339 <option value="haldane" selected="true">Haldane</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
340 <option value="kosambi" >Kosambi</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
341 </param>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
342 <param name="extra_scan_units" type="select" label="Output units" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
343 <option value="cM" selected="true">CentiMorgans</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
344 <option value="rec-frac" >Recombination Fractions</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
345 </param>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
346 </section>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
347 <!-- End of display: Works -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
348
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
349 <!-- Range section -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
350 <section name="section_range" expanded="false" title="Range options" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
351 <conditional name="advanced_options_positions" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
352 <param name="extra_mod_positions" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Define custom position range" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
353 <when value="off" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
354 <when value="on" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
355 <param name="extra_mod_positions_lowest" type="float" value="0" min="0" max="1000" label="Lowest position (cM)" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
356 <param name="extra_mod_positions_highest" type="float" value="1" min="0" max="1000" label="Highest position (cM)" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
357 <!-- Assert: lowest < higher -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
358 </when>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
359 </conditional>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
360
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
361 <param name="extra_offend" type="float" value="0.0" label="Margin before and after marker range to compute scores (cM)" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
362
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
363 <conditional name="advanced_options_increment" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
364 <param name="extra_increment_type" type="select" label="Increment either the genetic distance across the whole range of markers, or the number of equally-spaced steps between adjacent markers" help="Note that the total number of steps (markers * calc. per step) must not exceed 1000." >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
365 <option value="distance" >Distance</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
366 <option value="steps" selected="true" >Steps</option>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
367 </param>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
368 <when value="distance" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
369 <param name="extra_increment_sizepavu" type="float" min="1.0" value="1" max="1000" label="centiMorgan interval" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
370 </when>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
371 <when value="steps" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
372 <param name="extra_increment_sizepavu" type="integer" min="1" value="2" max="30" label="Number of steps between markers." />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
373 </when>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
374 </conditional>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
375
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
376 <param name="extra_maxbits" type="integer" min="3" value="19" max="30" label="Max bit-size of the pedigree, computed via '2N-F', for F founders and N non-founders" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
377 <param name="extra_maxbits_skiplarge" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Split pedigrees if larger than the max pedigree size" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
378 </section>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
379 <!-- End of range:Works -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
380
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
381 <!-- Frequency section -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
382 <section name="section_allfreq" title="Allele Frequency Options">
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
383 <param name="extra_nmaf" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Normalize Allele Frequencies" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
384
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
385 <param name="extra_mod_allfreq" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Restrict disease allele frequency" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
386
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
387 <param name="extra_mod_highallele" type="float" min="0" max="1" value="0.5" label="Set maximum disease allele frequency" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
388
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
389 <param name="extra_mod_penetrancerestrict" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Restrict Penetrances" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
390
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
391 </section>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
392 <!-- End of Frequency section:Works -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
393
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
394 <!-- Sample Individuals section -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
395 <section name="section_sample" title="Sample Options" >
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
396 <param name="extra_sun" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Simulate untyped individuals" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
397 <param name="extra_includeuntyped" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Include untyped individuals" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
398 <param name="extra_cpv_fin" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Process fully homozygous (uninformative) genotypes" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
399 <param name="extra_discard" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Discard uninformative individuals" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
400 <param name="extra_ufo" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use untyped founders" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
401 </section>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
402 <!-- End of sample individuals -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
403 </section>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
404 <!-- End of advanced options -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
405 </inputs>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
406
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
407 <outputs>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
408 <!-- All outputs convert to an Allegro format -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
409 <data name="ihaplo" format="allegro_ihaplo" label="${tool.name} on ${on_string}: Haplotypes" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
410 <data name="fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
411 </outputs>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
412
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
413 <tests>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
414 <test><!-- Defaults with haplo -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
415 <expand macro="test_input_files" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
416
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
417 <param name="extra_haplotype" value="on" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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418
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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419 <expand macro="test_output_fparam" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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420 <expand macro="test_output_haplo" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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421 </test>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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422 <test><!-- Haplotypes via Viterbi resolution -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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423 <expand macro="test_input_files" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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424
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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425 <param name="extra_mod_analysis" value="BOTH" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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426 <param name="extra_haplotype" value="on" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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427 <param name="extra_haplotype_method" value="Viterbi" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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428 <param name="extra_increment_sizepavu" value="10" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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429
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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430 <expand macro="test_output_haplo" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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431 <expand macro="test_output_fparam" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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432 </test>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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433 <test><!-- Parametric LOD with restricted scoring -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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434 <expand macro="test_input_files" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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435
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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436 <param name="extra_mod_allfreq" value="on" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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437 <param name="extra_mod_highallele" value="0.8" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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438 <param name="extra_npl_score" value="hom" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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439
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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440 <expand macro="test_output_fparam" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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441 </test>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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442 <test><!-- Haplo + Single IBS with computed founders -->
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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443 <expand macro="test_input_files" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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parents:
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444
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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445 <param name="extra_cpv_fin" value="on" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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446 <param name="extra_modcalc" value="single" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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447 <param name="extra_mod_bep" value="bep on" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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448 <param name="extra_srs" value="10" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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449
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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450 <expand macro="test_output_fparam" />
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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451 </test>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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452 </tests>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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453
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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454 <help><![CDATA[
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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455
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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456 **Genehunter-MODscore** calculates a *maximized LOD* (MOD) score over a set of genotypes for use in linkage and haplotype analysis.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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457
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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458 Haplotypes are generated using either this maximum probability approach, or via slower more conventional Viterbi crawling.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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459
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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460 Untyped founders can be simulated by reconstructing their haplotypes from offspring, and points of recombination can still be accurately determined in lieu of this.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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461
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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462 Due to the stochastic nature of the analysis, a random seed can be set by the user to produce reproducible results.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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463
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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464 Many more configurable options are outlined in the the official manual_.
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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465
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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466 .. _manual: https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.pdf
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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467
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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468 ]]>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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469 </help>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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470 <citations>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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471 <citation type="doi">10.1159/000369065</citation>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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parents:
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472 <citation type="doi">10.1002/gepi.20264</citation>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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473 <citation type="doi">10.1093/bioinformatics/btl539</citation>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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474 <citation type="doi">10.1186/1471-2156-6-S1-S162</citation>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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475 </citations>
9e6a43112688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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476 </tool>