Mercurial > repos > cropgeeks > flapjack
comparison creatematrix.xml @ 54:8855844f40a8 draft
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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| 53:1de63acd6b12 | 54:8855844f40a8 |
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| 1 <tool id="flapjack_creatematrix" name="Flapjack Create Similarity Matrix" version="0.0.1"> | |
| 2 <description>Create a similarity matrix from the given Genotype file</description> | |
| 3 <command><![CDATA[ | |
| 4 java | |
| 5 #if $adv_opts.show_advanced | |
| 6 -Xmx$adv_opts.memory | |
| 7 #end if | |
| 8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateMatrix | |
| 9 -g $genotypes | |
| 10 -o $output | |
| 11 #if $map | |
| 12 -m $map | |
| 13 #end if | |
| 14 #if $adv_opts.show_advanced | |
| 15 $adv_opts.allChromosomes | |
| 16 $adv_opts.collapseHets | |
| 17 -M "$adv_opts.missingData" | |
| 18 -S "$adv_opts.hetSep" | |
| 19 $adv_opts.transposed | |
| 20 $adv_opts.decimalEnglish | |
| 21 #end if | |
| 22 #if $create_project | |
| 23 -p $project | |
| 24 #end if | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param format="fjmap" name="map" type="data" label="Flapjack map file" | |
| 28 help="Flapjack-formatted (tab-delimited text) input file of map data" | |
| 29 optional="true"/> | |
| 30 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" | |
| 31 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> | |
| 32 | |
| 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.--> | |
| 34 <conditional name="adv_opts"> | |
| 35 <param name="show_advanced" type="boolean" | |
| 36 label="Enable advanced options" | |
| 37 truevalue="show" falsevalue=""> | |
| 38 </param> | |
| 39 <when value="show"> | |
| 40 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False" | |
| 41 label="Duplicate all markers onto a single 'All Chromosomes' chromosome" | |
| 42 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/> | |
| 43 | |
| 44 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True" | |
| 45 label="Don't distinguish between heterozygous alleles" | |
| 46 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/> | |
| 47 | |
| 48 <param name="missingData" type="text" value="-" | |
| 49 label="Missing data string" | |
| 50 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> | |
| 51 | |
| 52 <param name="hetSep" type="text" value="/" | |
| 53 label="Heterozygous allele separator string" | |
| 54 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> | |
| 55 | |
| 56 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False" | |
| 57 label="Genotype data has been transposed" | |
| 58 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/> | |
| 59 | |
| 60 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False" | |
| 61 label="Force English-style decimal marks" | |
| 62 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/> | |
| 63 | |
| 64 <param name="memory" type="select" | |
| 65 label="Memory" | |
| 66 help="How much memory to use (larger files may require more memory)."> | |
| 67 <option selected="true" value="64m">64MB</option> | |
| 68 <option value="128m">128MB</option> | |
| 69 <option value="256m">256MB</option> | |
| 70 </param> | |
| 71 </when> | |
| 72 </conditional> | |
| 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.--> | |
| 74 | |
| 75 <param name="create_project" type="boolean" label="Also create Flapjack project file" | |
| 76 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the generated similarity matrix."> | |
| 77 </param> | |
| 78 </inputs> | |
| 79 | |
| 80 <outputs> | |
| 81 <data format="tabular" name="output" /> | |
| 82 <data format="flapjack" name="project"> | |
| 83 <filter>create_project</filter> | |
| 84 </data> | |
| 85 </outputs> | |
| 86 | |
| 87 <stdio> | |
| 88 <exit_code range="1:" /> | |
| 89 </stdio> | |
| 90 | |
| 91 <help><![CDATA[ | |
| 92 .. class:: infomark | |
| 93 | |
| 94 **What it does** | |
| 95 | |
| 96 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, | |
| 97 allowing for rapid navigation and comparisons between lines, markers and chromosomes. | |
| 98 | |
| 99 Flapjack documentation_ | |
| 100 | |
| 101 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#creatematrix-exe-jhi-flapjack-io-creatematrix | |
| 102 ]]></help> | |
| 103 | |
| 104 <citations> | |
| 105 <citation type="doi">10.1093/bioinformatics/btq580</citation> | |
| 106 </citations> | |
| 107 </tool> |