Mercurial > repos > iuc > allegro

annotate allegro.xml @ 0:8c29e3621475 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
author iuc
date Sat, 09 Dec 2017 06:39:42 -0500
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8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
iuc
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1 <tool id="allegro" name="Allegro" version="@VER@.0" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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2 <description>Linkage and Haplotype analysis</description>
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3 <macros>
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4 <token name="@VER@">2</token>
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5 <xml name="macro_inputs" >
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6 <param name="inp_ped" value="pedin.21" />
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7 <param name="inp_dat" value="datain.21" />
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8 <param name="inp_map" value="map.21" />
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iuc
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9 </xml>
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10 </macros>
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11 <requirements>
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12 <requirement type="package" version="@VER@">allegro</requirement>
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13 </requirements>
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14 <version_command><![CDATA[
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15 allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
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16 ]]>
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17 </version_command>
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18 <command detect_errors='exit_code'>allegro $allegro_conf</command>
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19
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20 <configfiles>
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21 <configfile name="allegro_conf" ><![CDATA[
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22 PREFILE $inp_ped
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23 DATFILE $inp_dat
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24 #if $inp_map
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25 MAPFILE $inp_map
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26 #end if
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27
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28 #if $cond_haplotypes.opt_haplotypes == 'yes'
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29 HAPLOTYPE haplo.out ${out_ihaplo} ${out_founder} inher.out
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30 #if $cond_haplotypes.opt_crossover
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31 CROSSOVERRATE combined.out ${out_combined_cross}
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32 #end if
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33 #elif $cond_haplotypes.opt_haplotypes.value == 'no'
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34 #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
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35 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam}
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36
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37 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
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38 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
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39
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40 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'
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41 #if $cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.opt_custom_freqs.value == 'yes'
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42 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked} freq:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_freq pen:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_pen $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_par_het param.mpt ${out_fparam}
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43 #end if
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44 #end if
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45
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46 #if $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPS'
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47 STEPS $cond_haplotypes.section_linkage.cond_steps.extra_steps
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48 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPFILE'
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49 STEPFILE $cond_haplotypes.section_linkage.cond_steps.inp_stepfile
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50 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
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51 MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
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52 #end if
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53 #end if
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54
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55 #if $opt_xlinked.value == 'X'
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56 SEXSPECIFIC on
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57 #end if
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58
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59 ENTROPY ${opt_entropy}
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60 NPLEXACTP ${opt_nplexactp}
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61
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62 #if $cond_pairwise.opt_pairwise.value == 'yes'
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63 PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
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64 #end if
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65
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66
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67 #if $cond_sim.opt_sim.value == 'yes'
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68 SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
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69 #end if
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70
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71 MAXMEMORY 102400
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72 UNIT $opt_unit
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73
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74 UNINFORMATIVE
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75
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76
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77 ]]>
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78 </configfile>
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79 </configfiles>
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80
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81 <inputs>
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82 <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
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83 <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." />
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84 <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" optional="true" />
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85
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86 <conditional name="cond_haplotypes" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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parents:
diff changeset
87 <param name="opt_haplotypes" type="select" label="Use Haplotypes?" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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88 <option value="yes" >Yes</option>
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parents:
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89 <option value="no" selected="true" >No</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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diff changeset
90 </param>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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91
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92 <when value="yes" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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parents:
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93 <param name="opt_crossover" type="boolean" value="false" label="Show crossover rate" />
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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94 </when>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
iuc
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diff changeset
95 <when value="no" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
iuc
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96 <section name="section_linkage" title="Linkage" expanded="true" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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97 <param name="extra_linkage_mptspt" type="select" label="Use multipoint IBD sharing probabilities, instead of single point" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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98 <option value="mpt" selected="true" >mpt</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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99 <option value="spt" >spt</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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100 </param>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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101
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102 <conditional name="cond_linktype" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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103 <param name="extra_linkage_type" type="select" label="Type of analysis" >
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104 <option value="defaults" selected="true" >Defaults</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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105 <option value="allele_sharing" >Allele Sharing</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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106 <option value="classical" >Classical</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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107 </param>
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108
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109 <when value="defaults" />
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110
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111 <when value="allele_sharing">
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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112 <param name="extra_linkage_linexp" type="select" label="Linear or Exponential" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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113 <option value="lin" >Linear</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
iuc
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114 <option value="exp" >Exponential</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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115 </param>
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116 <param name="extra_linkage_scoring" type="select" label="Scoring function" >
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117 <option value="pairs">Pairs</option>
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118 <option value="all">All</option>
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119 <option value="homoz">Homozygous</option>
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120 <option value="mnallele">MNAllele</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
iuc
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121 <option value="robdom">RobDom</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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122 <option value="ps:mm/mf/ff">PS:MM/MF/FF</option>
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123 </param>
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124
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125 <param name="extra_weighting" type="select" label="Weighting function" >
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126 <option value="equal">Equal</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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127 <option value="power:0.5">Power</option>
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128 </param>
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129 </when>
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130
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131 <when value="classical" >
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132 <conditional name="cond_customfreqs" >
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133 <param name="opt_custom_freqs" type="select" label="Use custom frequencies instead of datafile" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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134 <option value="yes" >Yes</option>
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135 <option value="no" selected="true" >No</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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136 </param>
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137 <when value="no" />
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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138 <when value="yes" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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139 <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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140 <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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141 </when>
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142 </conditional>
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143 <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
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144 </when>
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145 </conditional>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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146
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147 <conditional name="cond_steps" >
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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148 <param name="extra_steps_type" type="select" label="Step Type" >
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149 <option value="STEPS">Calculations between adjacent markers</option>
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150 <option value="STEPFILE">Calculations at positions set in file</option>
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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151 <option value="MAXSTEPLENGTH">Calculations at periodic (cM) intervals</option>
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152 </param>
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153 <when value="STEPS">
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154 <param name="extra_steps" type="integer" min="1" value="2" label="# Steps" />
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155 </when>
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156 <when value="STEPFILE">
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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157 <param name="inp_stepfile" type="data" format="txt" label="Step file" />
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158 </when>
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159 <when value="MAXSTEPLENGTH">
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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160 <param name="extra_maxstep" type="float" min="1" value="2" label="cM" />
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161 </when>
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162 </conditional>
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163 </section>
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164 </when>
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165 </conditional>
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166
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167 <param name="opt_xlinked" type="select" label="Disease model" >
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168 <option value="">Autosomal</option>
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169 <option value="X">X-Linked</option>
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170 </param>
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171
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172 <param name="opt_entropy" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Entropy" />
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173 <param name="opt_nplexactp" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use exact P-values" />
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174
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175 <conditional name="cond_pairwise" >
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176 <param name="opt_pairwise" type="select" label="Perform Pairwise Analysis?" >
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177 <option value="yes" >Yes</option>
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178 <option value="no" selected="true" >No</option>
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179 </param>
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180
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181 <when value="no"/>
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182 <when value="yes" >
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183 <param name="extra_pairwise_type" type="select" label="Weighting" >
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184 <option value="all">All</option>
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185 <option value="genotype">Genotype</option>
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186 <option value="affected">Affected</option>
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187 <option value="informative">Informative</option>
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188 </param>
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189 </when>
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190 </conditional>
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191
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192 <conditional name="cond_sim" >
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193 <param name="opt_sim" type="select" label="Simulate multipoint data?" >
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194 <option value="yes" >Yes</option>
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195 <option value="no" selected="true" >No</option>
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196 </param>
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197 <when value="no" />
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198 <when value="yes" >
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199 <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
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200 <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
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201 <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
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202 <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
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203 <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
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204 <param name="extra_sim_het" type="float" value="0" label="HET probability" />
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205 </when>
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206 </conditional>
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207 <param name="opt_sexspecific" type="boolean" truevalue="on" falsevalue="off" value="false" label="Use Sex-Specific Penetrances (specified in data file)" help="Note that you will need to include sex-specific penetrances in your data input file for this to work." />
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208 <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
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209 </inputs>
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210
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211 <outputs>
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212 <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
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213 <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
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214 <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
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215 <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
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216 <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
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217 </outputs>
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218
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219 <tests>
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220 <test><!-- Default Haplotypes -->
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221 <expand macro="macro_inputs" />
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222
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223 <param name="extra_linkage_type" value="classical" />
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224 <param name="extra_linkage_mptspt" value="mpt" />
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225 <param name="opt_haplotypes" value="yes" />
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226
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227 <output name="out_ihaplo" >
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228 <assert_contents>
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229 <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
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230 </assert_contents>
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231 </output>
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232 </test>
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233 <test><!-- Linkage with custom steps-->
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234 <expand macro="macro_inputs" />
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235
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236 <param name="extra_linkage_type" value="classical" />
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237 <param name="extra_linkage_mptspt" value="mpt" />
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238 <param name="extra_linkage_mptspt" value="mpt" />
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239 <param name="extra_steps" value="3" />
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240 <param name="extra_maxstep" value="30" />
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241
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242
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243 <output name="out_fparam" >
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244 <assert_contents>
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245 <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
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246 </assert_contents>
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247 </output>
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248 </test>
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249 <test><!-- Single-point linear expression test with power weights -->
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250 <expand macro="macro_inputs" />
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251
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252 <param name="extra_linkage_type" value="allele_sharing" />
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253 <param name="extra_linkage_mptspt" value="spt" />
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254 <param name="extra_linkage_linexp" value="lin" />
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255 <param name="extra_linkage_scoring" value="homoz" />
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256 <param name="extra_weighting" value="power:50" />
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257
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258 <output name="out_fparam" >
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259 <assert_contents>
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260 <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
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261 </assert_contents>
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262 </output>
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263 </test>
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264 </tests>
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265 <help>
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266 Allegro is a computer program for multipoint genetic linkage analysis and related calculations. Allegro can do both classical parametric linkage analysis and analysis based on allele sharing models. In addition, Allegro estimates total number of recombinations between markers, computes posterior IBD sharing probabilities, re-constructs haplotypes and does two types of simulation. Thus Allegro includes the basic functionality of the well known Genehunter program (Kruglyak et al. 1996). It can analyse pedigrees of moderate size,and it can handle many markers. The biggest advantages of Allegro over Genehunterar the allele sharing models that it provides and a much shorter execution time.
8c29e3621475 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
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267 </help>
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268 <citations>
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269 <citation type="doi">10.1038/ng1005-1015</citation>
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270 <citation type="doi">10.1038/75514</citation>
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271 </citations>
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272 </tool>