Mercurial > repos > cropgeeks > flapjack

annotate creatematrix.xml @ 54:8855844f40a8 draft

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Uploaded the latest version of our Flapjack tools for Galaxy.
author cropgeeks
date Tue, 14 Nov 2017 06:42:48 -0500
parents
children 6777844fd638
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54
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy.
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1 <tool id="flapjack_creatematrix" name="Flapjack Create Similarity Matrix" version="0.0.1">
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2 <description>Create a similarity matrix from the given Genotype file</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.CreateMatrix
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9 -g $genotypes
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10 -o $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 $adv_opts.show_advanced
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15 $adv_opts.allChromosomes
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16 $adv_opts.collapseHets
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17 -M "$adv_opts.missingData"
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18 -S "$adv_opts.hetSep"
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19 $adv_opts.transposed
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20 $adv_opts.decimalEnglish
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21 #end if
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22 #if $create_project
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23 -p $project
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24 #end if
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25 ]]></command>
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26 <inputs>
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27 <param format="fjmap" name="map" type="data" label="Flapjack map file"
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28 help="Flapjack-formatted (tab-delimited text) input file of map data"
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29 optional="true"/>
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30 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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31 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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32
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33 <!-- 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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34 <conditional name="adv_opts">
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35 <param name="show_advanced" type="boolean"
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36 label="Enable advanced options"
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37 truevalue="show" falsevalue="">
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38 </param>
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39 <when value="show">
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40 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
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41 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
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42 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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43
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44 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
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45 label="Don't distinguish between heterozygous alleles"
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46 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
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47
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48 <param name="missingData" type="text" value="-"
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49 label="Missing data string"
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50 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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51
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52 <param name="hetSep" type="text" value="/"
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53 label="Heterozygous allele separator string"
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54 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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55
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56 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
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57 label="Genotype data has been transposed"
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58 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
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59
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60 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
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61 label="Force English-style decimal marks"
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62 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
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63
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64 <param name="memory" type="select"
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65 label="Memory"
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66 help="How much memory to use (larger files may require more memory).">
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67 <option selected="true" value="64m">64MB</option>
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68 <option value="128m">128MB</option>
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69 <option value="256m">256MB</option>
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70 </param>
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71 </when>
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72 </conditional>
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73 <!-- 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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74
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75 <param name="create_project" type="boolean" label="Also create Flapjack project file"
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76 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the generated similarity matrix.">
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77 </param>
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78 </inputs>
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79
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80 <outputs>
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81 <data format="tabular" name="output" />
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82 <data format="flapjack" name="project">
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83 <filter>create_project</filter>
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84 </data>
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85 </outputs>
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86
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87 <stdio>
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88 <exit_code range="1:" />
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89 </stdio>
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90
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91 <help><![CDATA[
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92 .. class:: infomark
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93
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94 **What it does**
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95
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96 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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97 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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98
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99 Flapjack documentation_
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100
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101 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#creatematrix-exe-jhi-flapjack-io-creatematrix
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102 ]]></help>
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103
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104 <citations>
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105 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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106 </citations>
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107 </tool>