Mercurial > repos > cropgeeks > flapjack
comparison splitbysample.xml @ 68:dc02f001fd09 draft
Uploaded
| author | cropgeeks |
|---|---|
| date | Wed, 21 Feb 2018 12:03:38 -0500 |
| parents | |
| children | 805b78c41bac |
comparison
equal
deleted
inserted
replaced
| 67:0a0a6be2d6b4 | 68:dc02f001fd09 |
|---|---|
| 1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1"> | |
| 2 <description>create a Flapjack project file from Flapjack formatted input files.</description> | |
| 3 <command><![CDATA[ | |
| 4 python $__tool_directory__/FlapjackProject.py | |
| 5 -j $__tool_directory__/lib/flapjack.jar | |
| 6 -g $genotypes | |
| 7 -s $traits | |
| 8 #if $map | |
| 9 -m $map | |
| 10 #end if | |
| 11 #if $name | |
| 12 -n $name | |
| 13 #end if | |
| 14 #if $qtls | |
| 15 -q $qtls | |
| 16 #end if | |
| 17 #if $adv_opts.show_advanced | |
| 18 -M "$adv_opts.missingData" | |
| 19 -S "$adv_opts.hetSep" | |
| 20 #end if | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" | |
| 25 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> | |
| 26 | |
| 27 <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file" | |
| 28 help="Flapjack-formatted (tab-delimited text) input file of phenotype data"/> | |
| 29 | |
| 30 <param format="fjmap" name="map" type="data" label="Flapjack map file" | |
| 31 help="Flapjack-formatted (tab-delimited text) input file of map data" | |
| 32 optional="true"/> | |
| 33 | |
| 34 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file" | |
| 35 help="Flapjack-formatted (tab-delimited text) input file of QTL data" | |
| 36 optional="true"/> | |
| 37 | |
| 38 <!-- 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.--> | |
| 39 <conditional name="adv_opts"> | |
| 40 <param name="show_advanced" type="boolean" | |
| 41 label="Enable advanced options" | |
| 42 truevalue="show" falsevalue=""> | |
| 43 </param> | |
| 44 <when value="show"> | |
| 45 <param name="missingData" type="text" value="-" | |
| 46 label="Missing data string" | |
| 47 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> | |
| 48 | |
| 49 <param name="hetSep" type="text" value="/" | |
| 50 label="Heterozygous allele separator string" | |
| 51 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 <!-- 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.--> | |
| 55 </inputs> | |
| 56 | |
| 57 <outputs> | |
| 58 <data name="output" format="flapjack" /> | |
| 59 </outputs> | |
| 60 | |
| 61 <stdio> | |
| 62 <exit_code range="1:" /> | |
| 63 </stdio> | |
| 64 | |
| 65 <help><![CDATA[ | |
| 66 .. class:: infomark | |
| 67 | |
| 68 **What it does** | |
| 69 | |
| 70 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, | |
| 71 allowing for rapid navigation and comparisons between lines, markers and chromosomes. | |
| 72 | |
| 73 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files. | |
| 74 See Flapjack's documentation_ for more details on the various Flapjack data formats. | |
| 75 More information on the CreateProject tool can be found here_ | |
| 76 | |
| 77 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html | |
| 78 .. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject | |
| 79 ]]></help> | |
| 80 | |
| 81 <citations> | |
| 82 <citation type="doi">10.1093/bioinformatics/btq580</citation> | |
| 83 </citations> | |
| 84 </tool> |