flapjack: pedverf1stats.xml annotate

annotate pedverf1stats.xml @ 60:33eaa535ceb4 draft

Uploaded

author	cropgeeks
date	Wed, 21 Feb 2018 08:47:54 -0500
parents	8a06f49972d0
children

rev	line source
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	1 <tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
55 6777844fd638 Updated the descriptions of the Flapjack tools to be more consistent. cropgeeks parents: 54 diff changeset	2 <description>run pedigree verification of F1s (known parents) analysis on a dataset</description>
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	3 <command><![CDATA[
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	4 java
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	5 #if $adv_opts.show_advanced
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	6 -Xmx$adv_opts.memory
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	7 #end if
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	9 -m $map
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	10 -g $genotypes
56 8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	11 #if $qtls
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	12 -q $qtls
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	13 #end if
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	14 #if $traits
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	15 -t $traits
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	16 #end if
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	17 -f $parent1
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	18 -s $parent2
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	19 -o $output
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	20 #if $simulate_f1.simulate_f1_selector == False
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	21 -e $simulate_f1.expectedF1
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	22 #end if
60 33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	23 #if $exclude_parents
33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	24 -x
33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	25 #end if
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	26 #if $adv_opts.show_advanced
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	27 $adv_opts.allChromosomes
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	28 $adv_opts.collapseHets
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	29 -M "$adv_opts.missingData"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	30 -S "$adv_opts.hetSep"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	31 $adv_opts.transposed
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	32 $adv_opts.decimalEnglish
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	33 #end if
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	34 #if $create_project
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	35 -p $project
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	36 #end if
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	37 ]]></command>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	38 <inputs>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	39 <param format="fjmap" name="map" type="data" label="Flapjack map file"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	40 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	41
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	42 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	43 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	44
56 8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	45 <param format="fjqtl" name="qtls" type="data"
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	46 label="Flapjack QTL file"
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	47 help="Flapjack-formatted (tab-delimited text) input file of QTL data."
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	48 optional="true"/>
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	49
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	50 <param format="fjphenotype" name="traits" type="data"
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	51 label="Flapjack Trait file"
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	52 help="Flapjack-formatted (tab-delimited text) input file of trait data."
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	53 optional="true"/>
8a06f49972d0 Added more optional parameters to mabcstats.xml and pedverf1stats.xml cropgeeks parents: 55 diff changeset	54
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	55 <param name="parent1" type="integer" value="1" label="Index of parent 1"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	56 help="The index of the first parent in the genotype file"/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	57
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	58 <param name="parent2" type="integer" value="2" label="Index of parent 2"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	59 help="The index of the second parent in the genotype file"/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	60
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	61 <conditional name="simulate_f1">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	62 <param name="simulate_f1_selector" type="boolean" label="Simulate expected F1 (or use F1 from file)"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	63 truevalue="" falsevalue="show" checked="true">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	64 </param>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	65 <when value="show">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	66 <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	67 help="The index of the donor parent in the genotype file"/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	68 </when>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	69 </conditional>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	70
60 33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	71 <param name="exclude_parents" type="boolean" label="Exclude parental lines which have not been selected."
33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	72 truevalue="true" falsevalue="false" help="Excludes parental lines which have not been selected as the recurrent, or donor parent from the analysis and results.">
33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	73 </param>
33eaa535ceb4 Uploaded cropgeeks parents: 56 diff changeset	74
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	75 <!-- 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.-->
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	76 <conditional name="adv_opts">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	77 <param name="show_advanced" type="boolean"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	78 label="Enable advanced options"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	79 truevalue="show" falsevalue="">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	80 </param>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	81 <when value="show">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	82 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	83 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	84 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	85
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	86 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	87 label="Don't distinguish between heterozygous alleles"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	88 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	89
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	90 <param name="missingData" type="text" value="-"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	91 label="Missing data string"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	92 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	93
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	94 <param name="hetSep" type="text" value="/"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	95 label="Heterozygous allele separator string"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	96 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	97
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	98 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	99 label="Genotype data has been transposed"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	100 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	101
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	102 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	103 label="Force English-style decimal marks"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	104 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	105
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	106 <param name="memory" type="select"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	107 label="Memory"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	108 help="How much memory to use (larger files may require more memory).">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	109 <option selected="true" value="64m">64MB</option>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	110 <option value="128m">128MB</option>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	111 <option value="256m">256MB</option>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	112 </param>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	113 </when>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	114 </conditional>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	115 <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	116 <param name="create_project" type="boolean" label="Also create Flapjack project file"
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	117 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the pedigree verification of F1s (known parents) results.">
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	118 </param>
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	119 </inputs>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	120
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	121 <outputs>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	122 <data format="tabular" name="output" />
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	123 <data format="flapjack" name="project">
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	124 <filter>create_project</filter>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	125 </data>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	126 </outputs>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	127
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	128 <stdio>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	129 <exit_code range="1:" />
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	130 </stdio>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	131
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	132 <help><![CDATA[
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	133 .. class:: infomark
8970bd921458 Uploaded cropgeeks parents: diff changeset	134
8970bd921458 Uploaded cropgeeks parents: diff changeset	135 What it does
8970bd921458 Uploaded cropgeeks parents: diff changeset	136
8970bd921458 Uploaded cropgeeks parents: diff changeset	137 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
8970bd921458 Uploaded cropgeeks parents: diff changeset	138 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
8970bd921458 Uploaded cropgeeks parents: diff changeset	139
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	140 Flapjack documentation_
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	141
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	142 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#pedverf1stats-exe-jhi-flapjack-io-generatepedverf1sstats
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	143 ]]></help>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	144
54 8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	145 <citations>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	146 <citation type="doi">10.1093/bioinformatics/btq580</citation>
8855844f40a8 Uploaded the latest version of our Flapjack tools for Galaxy. cropgeeks parents: 41 diff changeset	147 </citations>
4 8970bd921458 Uploaded cropgeeks parents: diff changeset	148 </tool>

Mercurial > repos > cropgeeks > flapjack

annotate pedverf1stats.xml @ 60:33eaa535ceb4 draft