Mercurial > repos > iuc > genehunter_modscore

annotate genehunter_modscore.xml @ 0:a84f5184784f 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 05:57:27 -0500
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a84f5184784f 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" >
a84f5184784f 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>
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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>
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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>
a84f5184784f 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}
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
86 #else
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
87 score all
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
88 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
89
a84f5184784f 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
a84f5184784f 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}
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
93 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
94
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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96 ## Algebraic calculation for P-values, default on
a84f5184784f 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
a84f5184784f 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}
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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101 ## #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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102
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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106 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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107
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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110 ## #try
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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112 ## #except AssertionError
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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114 ## #end try
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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116 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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117
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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119 #if $section_haplo.analysis_haplo.extra_haplotype or $section_options.section_sample.extra_includeuntyped
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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121 #else:
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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122 include untyped off
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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123 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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124
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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127
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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130
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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133
a84f5184784f 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)
a84f5184784f 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
a84f5184784f 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
a84f5184784f 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 )
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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139 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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140
a84f5184784f 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 )
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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143
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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145 naf ${section_options.section_allfreq.extra_nmaf}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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146
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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147 ## off by default
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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148 #if '${section_options.section_pvalues.advanced_options_modcalc.extra_modcalc}' == 'single':
a84f5184784f 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.
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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151 #if not('${extra_alg}'):
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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152 #if '${extra_mod_savedmodels}'!=-1:
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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154 #end if
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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156
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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diff changeset
157 ## Long output for modcalc single
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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159
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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162 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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163
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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164
a84f5184784f 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
a84f5184784f 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
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
169 #if $section_options.section_pvalues.advanced_options_calcpval.extra_cpv_nor > 0
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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171 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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172 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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173
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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176
a84f5184784f 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
a84f5184784f 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)
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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179
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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182 sun on
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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183 #else
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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184 sun off
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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185 #end if
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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186
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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189
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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192
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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193 #### General
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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196
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197 ## Do not skip fully homozygous markers when generating haplotypes, default off
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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199
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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202
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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205
a84f5184784f 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
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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209
a84f5184784f 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
a84f5184784f 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}
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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214
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215 ## Max pedigree size calculated by 2N - F, default 19, trim individuals beyond this
a84f5184784f 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}
a84f5184784f 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
a84f5184784f 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}
a84f5184784f 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
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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221
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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222
a84f5184784f 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}
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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225 use
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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226
a84f5184784f 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}
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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228
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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231 ## - 'stat'
a84f5184784f 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
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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234
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235
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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236 ## TODO:
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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238 q
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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239 ]]>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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240 </configfile>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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241 </configfiles>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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242 <inputs>
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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246
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247 <section name="section_haplo" title="Haplotypes" expanded="true" >
a84f5184784f 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" >
a84f5184784f 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" />
a84f5184784f 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">
a84f5184784f 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." >
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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258 </section>
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259
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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260 <section name="section_linkage" title="Linkage" expanded="false" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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261 <param name="extra_singlepoint" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Single-point Analysis"/>
a84f5184784f 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" >
a84f5184784f 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" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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264 <option value="BOTH" selected="true" >Both</option>
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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267 </param>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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268 <when value="BOTH" ><expand macro="macro_npl_opts" /></when>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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269 <when value="NPL" ><expand macro="macro_npl_opts" /></when>
a84f5184784f 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>
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272 </section>
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273
a84f5184784f 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" >
a84f5184784f 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" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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279 <param name="extra_alg" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use Algebraic calculations for P-Values"/>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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280
a84f5184784f 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" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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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" />
a84f5184784f 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" />
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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289 <conditional name="advanced_options_model" >
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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298 <conditional name="advanced_options_calcpval" >
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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300
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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301 <when value="on" >
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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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iuc
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307
a84f5184784f 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" >
a84f5184784f 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" >
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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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" />
a84f5184784f 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" />
a84f5184784f 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
a84f5184784f 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" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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324 <option value="pre" >Pre</option>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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325 <option value="both" >Both</option>
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326 <option value="off" selected="true" >Off</option>
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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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" />
a84f5184784f 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" >
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
341 </param>
a84f5184784f 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" >
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
345 </param>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
346 </section>
a84f5184784f 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 -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
348
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
349 <!-- Range section -->
a84f5184784f 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" >
a84f5184784f 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" >
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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" >
a84f5184784f 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)" />
a84f5184784f 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)" />
a84f5184784f 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 -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
358 </when>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
359 </conditional>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
360
a84f5184784f 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)" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
362
a84f5184784f 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" >
a84f5184784f 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." >
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
367 </param>
a84f5184784f 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" >
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
370 </when>
a84f5184784f 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" >
a84f5184784f 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." />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
373 </when>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
374 </conditional>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
375
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
378 </section>
a84f5184784f 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 -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
380
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
381 <!-- Frequency section -->
a84f5184784f 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">
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
384
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
386
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
388
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
390
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
391 </section>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
392 <!-- End of Frequency section:Works -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
393
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
394 <!-- Sample Individuals section -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
395 <section name="section_sample" title="Sample Options" >
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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396 <param name="extra_sun" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Simulate untyped individuals" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
398 <param name="extra_cpv_fin" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Process fully homozygous (uninformative) genotypes" />
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
401 </section>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
402 <!-- End of sample individuals -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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403 </section>
a84f5184784f 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 -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
405 </inputs>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
406
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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diff changeset
407 <outputs>
a84f5184784f 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 -->
a84f5184784f 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 ${on_string}: Haplotypes" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
410 <data name="fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
411 </outputs>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
412
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
413 <tests>
a84f5184784f 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 -->
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
diff changeset
416
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
parents:
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418
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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420 <expand macro="test_output_haplo" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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421 </test>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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422 <test><!-- Haplotypes via Viterbi resolution -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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423 <expand macro="test_input_files" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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424
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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425 <param name="extra_mod_analysis" value="BOTH" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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426 <param name="extra_haplotype" value="on" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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427 <param name="extra_haplotype_method" value="Viterbi" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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428 <param name="extra_increment_sizepavu" value="10" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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429
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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432 </test>
a84f5184784f 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 -->
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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435
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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437 <param name="extra_mod_highallele" value="0.8" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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438 <param name="extra_npl_score" value="hom" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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439
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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441 </test>
a84f5184784f 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 -->
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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443 <expand macro="test_input_files" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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444
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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448 <param name="extra_srs" value="10" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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449
a84f5184784f 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" />
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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451 </test>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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452 </tests>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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453
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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454 <help><![CDATA[
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
iuc
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455
a84f5184784f 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.
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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457
a84f5184784f 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.
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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459
a84f5184784f 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.
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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461
a84f5184784f 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.
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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463
a84f5184784f 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_.
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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465
a84f5184784f 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
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467
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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468 ]]>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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469 </help>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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470 <citations>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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472 <citation type="doi">10.1002/gepi.20264</citation>
a84f5184784f 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>
a84f5184784f 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>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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475 </citations>
a84f5184784f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ commit bf4a43ac2ae894eeeb6e608badb6ea7f8288c8d9
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476 </tool>