Mercurial > repos > cropgeeks > flapjack
comparison hdf52fj.xml @ 54:8855844f40a8 draft
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 |
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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> |