Mercurial > repos > cropgeeks > flapjack

comparison hdf52fj.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 927533e85a6a
children 6777844fd638
comparison
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53:1de63acd6b12 54:8855844f40a8
1 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1"> 1 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1">
2 <description>Convert an HDF5 formatted genotype file into a Flapjack-formatted 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.Hdf5ToFJTabbedConverter
9 -h $hdf5
10 -o $genotypes
11 #if $lines
12 -l $lines
13 #end if
14 #if $markers
15 -m $markers
16 #end if
17 ]]></command>
18 <inputs>
19 <param format="h5" name="hdf5" type="data" label="A Flapjack HDF5 genotype file"
20 help="Flapjack's flavour of HDF5 for storing genotype data."/>
21 <param format="txt" name="lines" type="data" label="Line file"
22 help="A list of lines desired in the output. One line name per line on each line of the file."
23 optional="true"/>
24 <param format="txt" name="markers" type="data" label="Marker file"
25 help="A list of markers desired in the output. One line name per marker on each line of the file."
26 optional="true"/>
2 27
3 <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description> 28 <conditional name="adv_opts">
4 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter 29 <param name="show_advanced" type="boolean"
5 -hdf5=$hdf5 30 label="Enable advanced options"
6 -lines=$lines 31 truevalue="show" falsevalue="">
7 -markers=$markers 32 </param>
8 -missing_filter=$missing_filter 33 <when value="show">
9 -heterozygous_filter=$heterozygous_filter 34 <param name="memory" type="select"
10 -genotypes=$genotypes 35 label="Memory"
11 </command> 36 help="How much memory to use (larger files may require more memory).">
12 <inputs> 37 <option selected="true" value="64m">64MB</option>
13 <param format="h5" name="hdf5" type="data" label="Source file" 38 <option value="128m">128MB</option>
14 help="Flapjack's flavour of HDF5 for storing genotype data."/> 39 <option value="256m">256MB</option>
15 <param format="txt" name="lines" type="data" label="Source file" 40 </param>
16 help="A list of lines desired in the output. One line name per line on each line of the file."/> 41 </when>
17 <param format="txt" name="markers" type="data" label="Source file" 42 </conditional>
18 help="A list of markers desired in the output. One line name per marker on each line of the file."/> 43 </inputs>
19 <param name="missing_filter" type="boolean" label="Filter out missing markers"
20 truevalue="true" falsevalue="false">
21 </param>
22 <param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
23 truevalue="true" falsevalue="false">
24 </param>
25 <param name="memory" type="select" label="Memory"
26 help="How much memory to use; larger files may require more memory">
27 <option selected="true" value="64m">64MB</option>
28 <option value="128m">128MB</option>
29 <option value="256m">256MB</option>
30 </param>
31 </inputs>
32 <outputs>
33 <data format="fjgenotype" name="genotypes" />
34 </outputs>
35 44
36 <help><![CDATA[ 45 <outputs>
46 <data format="fjgenotype" name="genotypes" />
47 </outputs>
48
49 <stdio>
50 <exit_code range="1:" />
51 </stdio>
52
53 <help><![CDATA[
37 .. class:: infomark 54 .. class:: infomark
38 55
39 **What it does** 56 **What it does**
40 57
41 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, 58 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
42 allowing for rapid navigation and comparisons between lines, markers and chromosomes. 59 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
43 60
44 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. 61 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
45 See Flapjack's documentation_ for more details on the various Flapjack data formats. 62 See Flapjack's documentation_ for more details on the various Flapjack data formats.
46 63
47 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 64 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
65 ]]></help>
48 66
49 67 <citations>
50 68 <citation type="doi">10.1093/bioinformatics/btq580</citation>
51 ]]></help> 69 </citations>
52 <citations>
53 <citation type="doi">10.1093/bioinformatics/btq580</citation>
54 </citations>
55 </tool> 70 </tool>