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1 <tool id="intertek_flapjack_snp_sample_processor" name="Intertek / Flapjack - SNP Sample File Processor" 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.IntertekFlapjackSnpSampleFileProcessor
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9 -g $genotype
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10 -i $intertek
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11 -o $output
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12 ]]></command>
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13 <inputs>
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14 <param format="txt" name="intertek" type="data" label="Favourable allele file"
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15 help="An Intertek file with favourable and unfavourable allele information for markers."/>
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16 <param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file"
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17 help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can
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18 add the favourable and unfavourable allele information to this Flapjack genotype file."
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19 optional="true"/>
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20
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21 <conditional name="adv_opts">
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22 <param name="show_advanced" type="boolean"
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23 label="Enable advanced options"
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24 truevalue="show" falsevalue="">
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25 </param>
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26 <when value="show">
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27 <param name="memory" type="select"
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28 label="Memory"
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29 help="How much memory to use (larger files may require more memory).">
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30 <option selected="true" value="64m">64MB</option>
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31 <option value="128m">128MB</option>
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32 <option value="256m">256MB</option>
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33 </param>
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34 </when>
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35 </conditional>
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36 </inputs>
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37
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38 <outputs>
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39 <data format="fjgenotype" name="output" />
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40 </outputs>
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41
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42 <stdio>
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43 <exit_code range="1:" />
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44 </stdio>
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45
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46 <help><![CDATA[
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47 .. class:: infomark
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48
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49 **What it does**
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50
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51 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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52 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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53
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54 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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55 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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56
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57 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
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58 ]]></help>
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59
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60 <citations>
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61 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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62 </citations>
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63 </tool> |
