Mercurial > repos > cropgeeks > intertektoflapjack
changeset 3:11105e2e14ec draft default tip
Uploaded
| author | cropgeeks |
|---|---|
| date | Wed, 21 Feb 2018 07:03:31 -0500 |
| parents | 89bff8c2ef78 |
| children | |
| files | favalleleheadercreator.xml galaxy/favalleleheadercreator.xml galaxy/lib/commons-cli-1.4.jar galaxy/lib/intertek-parser.jar lib/commons-cli-1.4.jar lib/intertek-parser.jar |
| diffstat | 6 files changed, 63 insertions(+), 63 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/favalleleheadercreator.xml Wed Feb 21 07:03:31 2018 -0500 @@ -0,0 +1,63 @@ +<tool id="intertek_to_flapjack_fav_allele" name="Intertek -> Flapjack favourable allele header formate" version="0.0.1"> + <description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/intertek-parser.jar jhi.intertekparser.IntertekParser + -g $genotype + -i $intertek + -o $output + ]]></command> + <inputs> + <param format="txt" name="intertek" type="data" label="Intertek favourable allele file" + help="An Intertek file with favourable and unfavourable allele information for markers."/> + <param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file" + help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can + add the favourable and unfavourable allele information to this Flapjack genotype file." + optional="true"/> + + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="memory" type="select" + label="Memory" + help="How much memory to use (larger files may require more memory)."> + <option selected="true" value="64m">64MB</option> + <option value="128m">128MB</option> + <option value="256m">256MB</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data format="fjgenotype" name="output" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, +allowing for rapid navigation and comparisons between lines, markers and chromosomes. + +This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. +See Flapjack's documentation_ for more details on the various Flapjack data formats. + +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html + ]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> +</tool> \ No newline at end of file
--- a/galaxy/favalleleheadercreator.xml Wed Feb 21 04:45:14 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -<tool id="intertek_to_flapjack_fav_allele" name="Intertek -> Flapjack favourable allele header formate" version="0.0.1"> - <description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description> - <command><![CDATA[ - java - #if $adv_opts.show_advanced - -Xmx$adv_opts.memory - #end if - -cp $__tool_directory__/lib/intertek-parser.jar jhi.intertekparser.IntertekParser - -g $genotype - -i $intertek - -o $output - ]]></command> - <inputs> - <param format="txt" name="intertek" type="data" label="Intertek favourable allele file" - help="An Intertek file with favourable and unfavourable allele information for markers."/> - <param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file" - help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can - add the favourable and unfavourable allele information to this Flapjack genotype file." - optional="true"/> - - <conditional name="adv_opts"> - <param name="show_advanced" type="boolean" - label="Enable advanced options" - truevalue="show" falsevalue=""> - </param> - <when value="show"> - <param name="memory" type="select" - label="Memory" - help="How much memory to use (larger files may require more memory)."> - <option selected="true" value="64m">64MB</option> - <option value="128m">128MB</option> - <option value="256m">256MB</option> - </param> - </when> - </conditional> - </inputs> - - <outputs> - <data format="fjgenotype" name="output" /> - </outputs> - - <stdio> - <exit_code range="1:" /> - </stdio> - - <help><![CDATA[ -.. class:: infomark - -**What it does** - -Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, -allowing for rapid navigation and comparisons between lines, markers and chromosomes. - -This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. -See Flapjack's documentation_ for more details on the various Flapjack data formats. - -.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html - ]]></help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> -</tool> \ No newline at end of file