Mercurial > repos > cropgeeks > flapjack

comparison fj2hdf5.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 8970bd921458
children 6777844fd638
comparison
equal deleted inserted replaced
53:1de63acd6b12 54:8855844f40a8
1 <tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1"> 1 <tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
2 <description>convert a Flapjack-formatted genotype file into HDF5</description> 2 <description>Convert a Flapjack-formatted genotype file into HDF5</description>
3 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command> 3 <command><![CDATA[
4 <inputs> 4 java
5 <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file" 5 #if $adv_opts.show_advanced
6 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> 6 -Xmx$adv_opts.memory
7 <param name="memory" type="select" label="Memory" 7 #end if
8 help="How much memory to use; larger files may require more memory"> 8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter
9 <option selected="true" value="64m">64MB</option> 9 -g $genotypes
10 <option value="128m">128MB</option> 10 -h $output
11 <option value="256m">256MB</option> 11 ]]></command>
12 </param> 12 <inputs>
13 </inputs> 13 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
14 <outputs> 14 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
15 <data format="h5" name="output_hdf5" />
16 </outputs>
17 15
18 <help><![CDATA[ 16 <conditional name="adv_opts">
17 <param name="show_advanced" type="boolean"
18 label="Enable advanced options"
19 truevalue="show" falsevalue="">
20 </param>
21 <when value="show">
22 <param name="memory" type="select"
23 label="Memory"
24 help="How much memory to use (larger files may require more memory).">
25 <option selected="true" value="64m">64MB</option>
26 <option value="128m">128MB</option>
27 <option value="256m">256MB</option>
28 </param>
29 </when>
30 </conditional>
31 </inputs>
32
33 <outputs>
34 <data format="h5" name="output" />
35 </outputs>
36
37 <stdio>
38 <exit_code range="1:" />
39 </stdio>
40
41 <help><![CDATA[
19 .. class:: infomark 42 .. class:: infomark
20 43
21 **What it does** 44 **What it does**
22 45
23 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, 46 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
24 allowing for rapid navigation and comparisons between lines, markers and chromosomes. 47 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
25 48
26 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. 49 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
27 See Flapjack's documentation_ for more details on the various Flapjack data formats. 50 See Flapjack's documentation_ for more details on the various Flapjack data formats.
28 51
29 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 52 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
53 ]]></help>
30 54
31 55 <citations>
32 56 <citation type="doi">10.1093/bioinformatics/btq580</citation>
33 ]]></help> 57 </citations>
34 <citations>
35 <citation type="doi">10.1093/bioinformatics/btq580</citation>
36 </citations>
37 </tool> 58 </tool>