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annotate createproject.xml @ 59:3ff3493f54d6 draft

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author cropgeeks
date Fri, 17 Nov 2017 06:38:55 -0500
parents 6777844fd638
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1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
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2 <description>create a Flapjack project file from Flapjack formatted input files.</description>
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3 <command><![CDATA[
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4 java
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5 #if $adv_opts.show_advanced
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6 -Xmx$adv_opts.memory
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7 #end if
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8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject
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9 -g $genotypes
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10 -p $output
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11 #if $map
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12 -m $map
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13 #end if
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14 #if $name
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15 -n $name
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16 #end if
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17 #if $qtls
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18 -q $qtls
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19 #end if
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20 #if $traits
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21 -t $traits
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22 #end if
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23 #if $adv_opts.show_advanced
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24 $adv_opts.allChromosomes
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25 $adv_opts.collapseHets
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26 -M "$adv_opts.missingData"
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27 -S "$adv_opts.hetSep"
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28 $adv_opts.transposed
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29 $adv_opts.decimalEnglish
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30 #end if
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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35 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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36
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37 <param format="fjmap" name="map" type="data" label="Flapjack map file"
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38 help="Flapjack-formatted (tab-delimited text) input file of map data"
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39 optional="true"/>
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40
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41 <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
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42 help="Flapjack-formatted (tab-delimited text) input file of phenotype data"
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43 optional="true"/>
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44
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45 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
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46 help="Flapjack-formatted (tab-delimited text) input file of QTL data"
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47 optional="true"/>
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48
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49 <param format="text" name="name" type="text" label="Optional dataset name"
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50 help="The name for the dataset within Flapjack"
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51 optional="true"/>
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52
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53 <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
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54 <conditional name="adv_opts">
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55 <param name="show_advanced" type="boolean"
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56 label="Enable advanced options"
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57 truevalue="show" falsevalue="">
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58 </param>
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59 <when value="show">
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60 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
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61 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
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62 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
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63
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64 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
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65 label="Don't distinguish between heterozygous alleles"
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66 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
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67
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68 <param name="missingData" type="text" value="-"
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69 label="Missing data string"
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70 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
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71
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72 <param name="hetSep" type="text" value="/"
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73 label="Heterozygous allele separator string"
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74 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
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75
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76 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
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77 label="Genotype data has been transposed"
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78 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
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79
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80 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
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81 label="Force English-style decimal marks"
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82 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
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83
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84 <param name="memory" type="select"
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85 label="Memory"
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86 help="How much memory to use (larger files may require more memory).">
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87 <option selected="true" value="64m">64MB</option>
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88 <option value="128m">128MB</option>
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89 <option value="256m">256MB</option>
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90 </param>
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91 </when>
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92 </conditional>
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93 <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
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94 </inputs>
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95
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96 <outputs>
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97 <data name="output" format="flapjack" />
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98 </outputs>
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99
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100 <stdio>
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101 <exit_code range="1:" />
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102 </stdio>
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103
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104 <help><![CDATA[
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105 .. class:: infomark
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106
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107 **What it does**
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108
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109 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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110 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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111
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112 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
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113 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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114 More information on the CreateProject tool can be found here_
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115
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116 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
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117 .. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
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118 ]]></help>
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119
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120 <citations>
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121 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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122 </citations>
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123 </tool>