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annotate hapmap2fj.xml @ 70:ca17d7295f9e draft

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author cropgeeks
date Thu, 22 Feb 2018 07:42:08 -0500
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1 <tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
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2 <description>convert a HapMap formatted file into a Flapjack formatted genotype file</description>
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3 <command><![CDATA[
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4 java
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5 #if $adv_opts.show_advanced
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6 -Xmx$adv_opts.memory
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7 #end if
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8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter
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9 -h $hapmap
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10 -s $separator
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11 -m $map
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12 -g $genotypes
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13 ]]></command>
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14 <inputs>
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15 <param format="txt" name="hapmap" type="data" label="Source file"
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16 help="HapMap Formatted File"/>
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18 <param name="separator" type="boolean" label="File is tab-separated"
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19 truevalue="t" falsevalue="s">
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20 </param>
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21
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22 <conditional name="adv_opts">
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23 <param name="show_advanced" type="boolean"
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24 label="Enable advanced options"
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25 truevalue="show" falsevalue="">
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26 </param>
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27 <when value="show">
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28 <param name="memory" type="select"
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29 label="Memory"
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30 help="How much memory to use (larger files may require more memory).">
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31 <option selected="true" value="64m">64MB</option>
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32 <option value="128m">128MB</option>
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33 <option value="256m">256MB</option>
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34 </param>
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35 </when>
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36 </conditional>
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37 </inputs>
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39 <outputs>
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40 <data format="fjmap" name="map" />
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41 <data format="fjgenotype" name="genotypes" />
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42 </outputs>
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43
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44 <stdio>
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45 <exit_code range="1:" />
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46 </stdio>
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47
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48 <help><![CDATA[
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49 .. class:: infomark
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50
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51 **What it does**
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52
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53 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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54 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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55
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56 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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57 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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59 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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60 ]]></help>
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62 <citations>
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63 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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64 </citations>
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65 </tool>