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comparison createproject.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 e8083821455b
children 6777844fd638
comparison
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53:1de63acd6b12 54:8855844f40a8
1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1"> 1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
2 <description>Create a Flapjack project file from the given input files.</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.CreateProject
9 -g $genotypes
10 -p $output
11 #if $map
12 -m $map
13 #end if
14 #if $name
15 -n $name
16 #end if
17 #if $qtls
18 -q $qtls
19 #end if
20 #if $traits
21 -t $traits
22 #end if
23 #if $adv_opts.show_advanced
24 $adv_opts.allChromosomes
25 $adv_opts.collapseHets
26 -M "$adv_opts.missingData"
27 -S "$adv_opts.hetSep"
28 $adv_opts.transposed
29 $adv_opts.decimalEnglish
30 #end if
31 ]]>
32 </command>
33 <inputs>
34 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
35 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
2 36
3 <!--System.out.println("Usage: createproject <options>\n" 37 <param format="fjmap" name="map" type="data" label="Flapjack map file"
4 + " where valid options are:\n" 38 help="Flapjack-formatted (tab-delimited text) input file of map data"
5 + " -map=<map_file> (optional input file)\n" 39 optional="true"/>
6 + " -genotypes=<genotypes_file> (required input file)\n"
7 + " -traits=<traits_file> (optional input file)\n"
8 + " -qtls=<qtl_file> (optional input file)\n"
9 + " -decimalEnglish (optional input parameter)\n"
10 + " -project=<project_file> (required output file)\n");-->
11 40
12 <description>Run pedigree verification of F1s (known parents) analysis</description> 41 <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
13 <command><![CDATA[ 42 help="Flapjack-formatted (tab-delimited text) input file of phenotype data"
14 java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject 43 optional="true"/>
15 -map=$map -genotypes=$genotypes
16 ## -galaxyHTML=$html
17 -project=$output
18 ]]>
19 </command>
20 <inputs>
21 <param format="fjmap" name="map" type="data" label="Flapjack map file"
22 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
23 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
24 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
25 44
26 <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" 45 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
27 label="Read input data using decimal English" 46 help="Flapjack-formatted (tab-delimited text) input file of QTL data"
28 help="Build the index using a perfect hash rather than a dense hash. This will require less memory 47 optional="true"/>
29 (especially during quantification), but will take longer to construct "/> 48
30 <param name="memory" type="select" label="Memory" 49 <param format="text" name="name" type="text" label="Optional dataset name"
31 help="How much memory to use; larger files may require more memory"> 50 help="The name for the dataset within Flapjack"
32 <option selected="true" value="64m">64MB</option> 51 optional="true"/>
33 <option value="128m">128MB</option> 52
34 <option value="256m">256MB</option> 53 <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
35 </param> 54 <conditional name="adv_opts">
36 </inputs> 55 <param name="show_advanced" type="boolean"
37 <outputs> 56 label="Enable advanced options"
38 <!-- label="${tool.name} on ${on_string}: project.flapjack" --> 57 truevalue="show" falsevalue="">
39 <data name="output" format="flapjack" /> 58 </param>
40 <!--<data name="html" format="html" />--> 59 <when value="show">
41 </outputs> 60 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
61 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
62 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
63
64 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
65 label="Don't distinguish between heterozygous alleles"
66 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
67
68 <param name="missingData" type="text" value="-"
69 label="Missing data string"
70 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
71
72 <param name="hetSep" type="text" value="/"
73 label="Heterozygous allele separator string"
74 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
75
76 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
77 label="Genotype data has been transposed"
78 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
79
80 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
81 label="Force English-style decimal marks"
82 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
83
84 <param name="memory" type="select"
85 label="Memory"
86 help="How much memory to use (larger files may require more memory).">
87 <option selected="true" value="64m">64MB</option>
88 <option value="128m">128MB</option>
89 <option value="256m">256MB</option>
90 </param>
91 </when>
92 </conditional>
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.-->
94 </inputs>
95
96 <outputs>
97 <data name="output" format="flapjack" />
98 </outputs>
42 99
43 <stdio> 100 <stdio>
44 <exit_code range="1:" /> 101 <exit_code range="1:" />
45 </stdio> 102 </stdio>
46 103
47 <help><![CDATA[ 104 <help><![CDATA[
48 .. class:: infomark 105 .. class:: infomark
49 106
50 **What it does** 107 **What it does**
51 108
52 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, 109 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
53 allowing for rapid navigation and comparisons between lines, markers and chromosomes. 110 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
54 111
55 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files. 112 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
56 See Flapjack's documentation_ for more details on the various Flapjack data formats. 113 See Flapjack's documentation_ for more details on the various Flapjack data formats.
114 More information on the CreateProject tool can be found here_
57 115
58 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 116 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
117 .. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
118 ]]></help>
59 119
60 120 <citations>
61 121 <citation type="doi">10.1093/bioinformatics/btq580</citation>
62 ]]></help> 122 </citations>
63 <citations>
64 <citation type="doi">10.1093/bioinformatics/btq580</citation>
65 </citations>
66 </tool> 123 </tool>