Mercurial > repos > cropgeeks > flapjack
comparison fj2hdf5.xml @ 54:8855844f40a8 draft
Uploaded the latest version of our Flapjack tools for Galaxy.
author | cropgeeks |
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date | Tue, 14 Nov 2017 06:42:48 -0500 |
parents | 8970bd921458 |
children | 6777844fd638 |
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53:1de63acd6b12 | 54:8855844f40a8 |
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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> |