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comparison hapmap2fj.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_hapmap2fj" name="HapMap to Flapjack" version="0.0.1"> 1 <tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
2 <description>Convert a HapMap-formatted 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.HapMapToFJTabbedConverter
9 -h $hapmap
10 -s $separator
11 -m $map
12 -g $genotypes
13 ]]></command>
14 <inputs>
15 <param format="txt" name="hapmap" type="data" label="Source file"
16 help="HapMap Formatted File"/>
2 17
3 <!--System.out.println("Usage: hapmap2flapjack <options>\n" 18 <param name="separator" type="boolean" label="File is tab-separated"
4 + " where valid options are:\n" 19 truevalue="t" falsevalue="s">
5 + " -separator=<s or t> (required separator used in input file)\n" 20 </param>
6 + " -hapmap=<hapmap_file> (required input file)\n"
7 + " -map=<map_file> (required output file)\n"
8 + " -genotypes=<genotype_file> (required output file)\n");-->
9 21
10 <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description> 22 <conditional name="adv_opts">
11 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter 23 <param name="show_advanced" type="boolean"
12 -hapmap=$hapmap 24 label="Enable advanced options"
13 -separator=$separator 25 truevalue="show" falsevalue="">
14 -map=$map 26 </param>
15 -genotypes=$genotypes 27 <when value="show">
16 </command> 28 <param name="memory" type="select"
17 <inputs> 29 label="Memory"
18 <param format="txt" name="hapmap" type="data" label="Source file" 30 help="How much memory to use (larger files may require more memory).">
19 help="HapMap Formatted File"/> 31 <option selected="true" value="64m">64MB</option>
20 <param name="separator" type="boolean" label="File is tab-separated" 32 <option value="128m">128MB</option>
21 truevalue="t" falsevalue="s"> 33 <option value="256m">256MB</option>
22 </param> 34 </param>
23 <param name="memory" type="select" label="Memory" 35 </when>
24 help="How much memory to use; larger files may require more memory"> 36 </conditional>
25 <option selected="true" value="64m">64MB</option> 37 </inputs>
26 <option value="128m">128MB</option>
27 <option value="256m">256MB</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data format="fjmap" name="map" />
32 <data format="fjgenotype" name="genotypes" />
33 </outputs>
34
35 <stdio>
36 <exit_code range="1:" />
37 </stdio>
38 38
39 <help><![CDATA[ 39 <outputs>
40 <data format="fjmap" name="map" />
41 <data format="fjgenotype" name="genotypes" />
42 </outputs>
43
44 <stdio>
45 <exit_code range="1:" />
46 </stdio>
47
48 <help><![CDATA[
40 .. class:: infomark 49 .. class:: infomark
41 50
42 **What it does** 51 **What it does**
43 52
44 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, 53 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
45 allowing for rapid navigation and comparisons between lines, markers and chromosomes. 54 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
46 55
47 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. 56 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
48 See Flapjack's documentation_ for more details on the various Flapjack data formats. 57 See Flapjack's documentation_ for more details on the various Flapjack data formats.
49 58
50 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 59 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
60 ]]></help>
51 61
52 62 <citations>
53 63 <citation type="doi">10.1093/bioinformatics/btq580</citation>
54 ]]></help> 64 </citations>
55 <citations>
56 <citation type="doi">10.1093/bioinformatics/btq580</citation>
57 </citations>
58 </tool> 65 </tool>