Mercurial > repos > iuc > bcftools_roh

annotate bcftools_roh.xml @ 0:b221ee100d2c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:08:58 -0400
parents
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0
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 <?xml version='1.0' encoding='utf-8'?>
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 <description>HMM model for detecting runs of autozygosity</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">roh</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15 ## General section
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16 #set $section = $sec_general
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17 @PREPARE_AF_FILE@
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18
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19 bcftools @EXECUTABLE@
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20
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 ## General section
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 #set $section = $sec_general
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23 @SAMPLE@
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24 @AF_FILE@
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25 #if $section.AF_tag:
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26 --AF-tag "${section.AF_tag}"
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 #end if
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28 #if $section.AF_dflt:
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29 --AF-dflt "${section.AF_dflt}"
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 #end if
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31 @ESTIMATE_AF@
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32 #if $section.GTs_only:
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33 --GTs-only "${section.GTs_only}"
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34 #end if
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35 ${section.skip_indels}
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36 #if $section.genetic_map:
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37 --genetic-map "${section.genetic_map}"
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38 #end if
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39 #if $section.rec_rate:
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40 --rec-rate "${section.rec_rate}"
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 #end if
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42
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43 ## HMM section
b221ee100d2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 #set $section = $sec_hmm
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45 #if $section.hw_to_az:
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46 --hw-to-az "${section.hw_to_az}"
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47 #end if
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48 #if $section.az_to_hw:
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49 --az-to-hw "${section.az_to_hw}"
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50 #end if
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51 ${section.viterbi_training}
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52
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53 ## General section
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54 #set $section = $sec_restrict
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55 @REGIONS@
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56 @TARGETS@
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57
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58 ## Primary Input/Outputs
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59 @INPUT_FILE@
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60 > "$output_file"
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61 ]]>
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62 </command>
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63 <inputs>
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64 <expand macro="macro_input" />
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65 <section name="sec_restrict" expanded="false" title="Restrict to">
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66 <expand macro="macro_regions" />
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67 <expand macro="macro_targets" />
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68 </section>
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69 <section name="sec_general" expanded="true" title="Roh General Options">
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70 <expand macro="macro_sample" />
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71 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True"
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72 help="Use the specified INFO tag TAG as an allele frequency estimate instead of the defaul AC and AN tags. Sites which do not have TAG will be skipped." />
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73 <param name="AF_dflt" type="float" value="" min="0." max="1." label="AF Default" optional="True" help="If AF is not known, use this allele frequency" />
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74 <expand macro="macro_AF_file" />
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75 <expand macro="macro_estimate_AF" />
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76 <param name="GTs_only" type="float" label="Gts Only" optional="True" help="Use GTs, ignore PLs, use &lt;float&gt; for PL of unseen genotypes. Safe value to use is 30 to account for GT errors." />
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77 <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
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78 <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
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79 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
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80 </section>
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81 <section name="sec_hmm" expanded="true" title="HMM Options">
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82 <param name="hw_to_az" type="float" label="Hw To Az" default="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
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83 <param name="az_to_hw" type="float" label="Az To Hw" default="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
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84 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
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85 </section>
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86 </inputs>
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87 <outputs>
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88 <data name="output_file" format="tabular"/>
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89 </outputs>
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90 <tests>
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91 <!-- Need an actual test input file -->
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92 <test>
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93 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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94 <param name="sample" value="HG00100" />
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95 <output name="output_file">
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96 <assert_contents>
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97 <has_text text="HG00100"/>
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98 <has_text text="State "/>
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99 </assert_contents>
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100 </output>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 =====================================
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105 bcftools @EXECUTABLE@
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106 =====================================
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107
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108 HMM model for detecting runs of autozygosity.
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109
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110 @REGIONS_HELP@
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111 @TARGETS_HELP@
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112
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113 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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114
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115 @BCFTOOLS_WIKI@
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116 ]]>
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117 </help>
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118 <expand macro="citations" />
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119 </tool>