Mercurial > repos > cropgeeks > flapjack
changeset 60:33eaa535ceb4 draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/favalleleheadercreator.xml Wed Feb 21 08:47:54 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.flapjack.io.cmd.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/mabcstats.xml Fri Nov 17 06:38:55 2017 -0500 +++ b/mabcstats.xml Wed Feb 21 08:47:54 2018 -0500 @@ -18,7 +18,7 @@ -c $coverage -o $output #if $exclude_parents - -e + -x #end if #if $adv_opts.show_advanced $adv_opts.allChromosomes
--- a/pedverf1stats.xml Fri Nov 17 06:38:55 2017 -0500 +++ b/pedverf1stats.xml Wed Feb 21 08:47:54 2018 -0500 @@ -20,6 +20,9 @@ #if $simulate_f1.simulate_f1_selector == False -e $simulate_f1.expectedF1 #end if + #if $exclude_parents + -x + #end if #if $adv_opts.show_advanced $adv_opts.allChromosomes $adv_opts.collapseHets @@ -65,6 +68,10 @@ </when> </conditional> + <param name="exclude_parents" type="boolean" label="Exclude parental lines which have not been selected." + truevalue="true" falsevalue="false" help="Excludes parental lines which have not been selected as the recurrent, or donor parent from the analysis and results."> + </param> + <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> <conditional name="adv_opts"> <param name="show_advanced" type="boolean"