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author cropgeeks
date Wed, 07 Mar 2018 08:04:25 -0500
parents 6777844fd638
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1 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1">
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2 <description>convert an HDF5 formatted genotype 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.Hdf5ToFJTabbedConverter
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9 -h $hdf5
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10 -o $genotypes
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11 #if $lines
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12 -l $lines
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13 #end if
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14 #if $markers
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15 -m $markers
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param format="h5" name="hdf5" type="data" label="A Flapjack HDF5 genotype file"
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20 help="Flapjack's flavour of HDF5 for storing genotype data."/>
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21 <param format="txt" name="lines" type="data" label="Line file"
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22 help="A list of lines desired in the output. One line name per line on each line of the file."
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23 optional="true"/>
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24 <param format="txt" name="markers" type="data" label="Marker file"
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25 help="A list of markers desired in the output. One line name per marker on each line of the file."
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26 optional="true"/>
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28 <conditional name="adv_opts">
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29 <param name="show_advanced" type="boolean"
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30 label="Enable advanced options"
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31 truevalue="show" falsevalue="">
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32 </param>
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33 <when value="show">
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34 <param name="memory" type="select"
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35 label="Memory"
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36 help="How much memory to use (larger files may require more memory).">
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37 <option selected="true" value="64m">64MB</option>
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38 <option value="128m">128MB</option>
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39 <option value="256m">256MB</option>
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40 </param>
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41 </when>
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42 </conditional>
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43 </inputs>
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45 <outputs>
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46 <data format="fjgenotype" name="genotypes" />
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47 </outputs>
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48
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49 <stdio>
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50 <exit_code range="1:" />
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51 </stdio>
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52
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53 <help><![CDATA[
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54 .. class:: infomark
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55
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56 **What it does**
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57
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58 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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59 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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60
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61 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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62 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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63
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64 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
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65 ]]></help>
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67 <citations>
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68 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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69 </citations>
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70 </tool>