plink: plink.xml annotate

annotate plink.xml @ 1:b8e3d957c0f5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 69a1f535817d0fe0406a448d885aafb8c0cce396"

author	iuc
date	Wed, 23 Sep 2020 08:05:17 +0000
parents	a98caf1d69ab
children	0d43871f45ac

rev	line source
0 a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	2 <macros>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	3 <token name='@TOOL_VERSION@'>1.9.b618</token>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	4 <token name='@VERSION_SUFFIX@'>0</token>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	5 <xml name='template_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	6 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	7 <valid initial='default'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	8 <add value='#' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	9 <add value='@' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	10 <add value='$'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	11 <add value='['/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	12 <add value=']'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	13 <add value='\'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	14 <remove value='"'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	15 <remove value='''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	16 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	17 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	18 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	19 <xml name='chr_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	20 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	21 <valid initial='string.digits'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	22 <add value='X' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	23 <add value='Y' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	24 <add value=' ' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	25 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	26 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	27 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	28 <xml name='snp_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	29 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	30 <valid initial='string.ascii_letters + string.digits'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	31 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	32 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	33 <xml name='snp_space_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	34 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	35 <valid initial='string.ascii_letters + string.digits'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	36 <add value=' '/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	37 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	38 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	39 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	40 </macros>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	41 <requirements>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	42 <requirement type='package' version='1.90b6.18'>plink</requirement>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	43 </requirements>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	44 <command detect_errors='exit_code'><![CDATA[
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	45
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	46 ## Create Plink folder for any inputs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	47 mkdir ./plink_output
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	48 && mkdir ./plink_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	49 #if $inputs.inputs.filetype == 'bfile':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	50 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	51 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	52 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	53 #elif $inputs.inputs.filetype == 'vcf':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	54 #if $inputs.inputs.input.is_of_type('vcf'):
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	55 && plink --vcf '$inputs.inputs.input'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	56 #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	57 && plink --bcf '$inputs.inputs.input'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	58 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	59 --out plink_input/plink_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	60 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	61
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	62 ## If bmerge is set, create folder for merged files
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	63 #if $functions.func == 'data_manage':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	64 #if $functions.bmerge.set == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	65 && mkdir bmerge_files
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	66 && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	67 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	68 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	69 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	70 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	71
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	72 ## Plink commands by section
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	73
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	74 && plink --bfile plink_input/plink_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	75 #if $inputs.covar_input:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	76 --covar '$inputs.covar_input'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	77 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	78 #if $inputs.pheno:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	79 --pheno $inputs.pheno
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	80 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	81 #if $functions.func == 'filtering':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	82 ##ID list functions
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	83 #if $functions.id_list.func == 'keep':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	84 --keep '$functions.id_list.file'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	85 #elif $functions.id_list.func == 'keep-fam':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	86 --keep-fam '$functions.id_list.file'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	87 #elif $functions.id_list.func == 'remove':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	88 --remove '$functions.id_list.file'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	89 #elif $functions.id_list.func == 'remove-fam':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	90 --remove-fam '$functions.id_list.file'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	91 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	92
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	93 ##Extraction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	94 #if $functions.extraction.ex_func == 'extract':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	95 --extract $functions.extraction.range $functions.extraction.file
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	96 #elif $functions.extraction.ex_func == 'exclude':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	97 --exclude $functions.extraction.range $functions.extraction.file
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	98 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	99
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	100 ##Chromosome-specificity
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	101 #if $functions.chromosome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	102 --chr $functions.chromosome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	103 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	104
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	105 #if $functions.excluded_chromosome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	106 --not-chr $functions.excluded_chromosome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	107 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	108
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	109 $functions.extra_chromosomes
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	110
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	111 #if $functions.autosome != 'none'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	112 $functions.autosome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	113 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	114
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	115 ##SNP specificity
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	116 #if $functions.snps_exclusives != 'No':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	117 --snps-only
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	118 #if $functions.snps_exclusives == 'acgt':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	119 'just-acgt'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	120 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	121 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	122
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	123 ##Variant windows
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	124 #if $functions.ranges.single_multi == 'single':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	125 #if $functions.ranges.window.type == 'variant':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	126 #if $functions.ranges.window.from:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	127 --from $functions.ranges.window.from
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	128 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	129 #if $functions.ranges.window.to:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	130 --to $functions.ranges.window.to
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	131 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	132 #elif $functions.ranges.window.type == 'window':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	133 #if $functions.ranges.window.snp:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	134 --snp $functions.ranges.window.snp
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	135 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	136 #if $functions.ranges.window.exclude_snp:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	137 --exclude-snp $functions.ranges.window.exclude_snp
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	138 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	139 #if $functions.ranges.window.window:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	140 --window $functions.ranges.window.window
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	141 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	142 #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	143 #if $functions.ranges.window.from_bp:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	144 --from-bp $functions.ranges.window.from_bp
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	145 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	146 #if $functions.ranges.window.to_bp:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	147 --to-bp $functions.ranges.window.to_bp
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	148 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	149 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	150 #elif $functions.ranges.single_multi == 'multi':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	151 $functions.ranges.force_intersect
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	152 #if $functions.ranges.snps:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	153 --snps $functions.ranges.snps
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	154 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	155 #if $functions.ranges.exclude_snps:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	156 --exclude-snps $functions.ranges.exclude_snps
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	157 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	158 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	159
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	160 ##Thinning
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	161 #if $functions.thinning.thinning == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	162 #if $functions.thinning.thin:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	163 --thin $functions.thinning.thin
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	164 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	165 #if $functions.thinning.thin_count:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	166 --thin-count $functions.thinning.thin_count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	167 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	168 #if $functions.thinning.bp_space:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	169 --bp-space $functions.thinning.bp_space
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	170 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	171 #if $functions.thinning.thin_indiv:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	172 --thin-indiv $functions.thinning.thin_indiv
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	173 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	174 #if $functions.thinning.thin_indiv_count:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	175 --thin-indiv-count $functions.thinning.thin_indiv_count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	176 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	177 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	178
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	179 ##Pheno/covariate
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	180 ###########
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	181
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	182 ###########
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	183
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	184 ##Missing genotype rates
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	185 #if $functions.geno_rates.geno:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	186 --geno $functions.geno_rates.geno
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	187 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	188 #if $functions.geno_rates.mind:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	189 --mind $functions.geno_rates.mind
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	190 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	191
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	192 ##Allele Frequencies
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	193 #if $functions.allele_freq.maf:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	194 --maf $functions.allele_freq.maf
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	195 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	196 #if $functions.allele_freq.max_maf:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	197 --max-maf $functions.allele_freq.max_maf
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	198 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	199 #if $functions.allele_freq.mac:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	200 --mac $functions.allele_freq.mac
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	201 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	202 #if $functions.allele_freq.max_mac:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	203 --max-mac $functions.allele_freq.max_mac
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	204 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	205
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	206 ## Hardy-Weinberg
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	207 #if $functions.hwe.hwe == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	208 --hwe $functions.hwe.hwe_val
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	209 #for $type in $functions.hwe.modifiers:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	210 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	211 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	212 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	213
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	214 ##Sex and Founder filter
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	215 #if $functions.sex_founder_filter.filter == 'Yes'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	216 $functions.sex_founder_filter.sex_select
1 b8e3d957c0f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 69a1f535817d0fe0406a448d885aafb8c0cce396" iuc parents: 0 diff changeset	217 #if $functions.sex_founder_filter.no_sex_select:
b8e3d957c0f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 69a1f535817d0fe0406a448d885aafb8c0cce396" iuc parents: 0 diff changeset	218 $functions.sex_founder_filter.no_sex_select
b8e3d957c0f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 69a1f535817d0fe0406a448d885aafb8c0cce396" iuc parents: 0 diff changeset	219 #end if
0 a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	220 $functions.sex_founder_filter.nonfounders
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	221 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	222
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	223 #elif $functions.func == 'data_manage':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	224
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	225 #if $functions.bmerge.set == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	226 --bmerge bmerge_files/bmerge_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	227 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	228
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	229 #if $functions.template:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	230 --set-missing-var-ids $functions.template
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	231 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	232
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	233 $functions.recode
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	234
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	235 #if $functions.flip:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	236 --flip $functions.flip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	237 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	238
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	239 #if $functions.length:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	240 --new-id-max-allele-len $functions.length
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	241 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	242
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	243 #if $functions.update_cols.set == 'update_map':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	244 --update-map $functions.update_cols.input $functions.update_cols.col_num $functions.update_cols.old_col $functions.update_cols.skip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	245 #elif $functions.update_cols.set == 'update_name':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	246 --update-name $functions.update_cols.input $functions.update_cols.col_num $functions.update_cols.var_col $functions.update_cols.skip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	247 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	248 #if $functions.ref_allele.set == 'yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	249 --reference-allele $functions.ref_allele.file $functions.ref_allele.column $functions.ref_allele.var_id $functions.ref_allele.skip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	250 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	251 #if $functions.a2_allele.set == 'yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	252 --a2-allele $functions.a2_allele.file $functions.a2_allele.column $functions.a2_allele.var_id $functions.a2_allele.skip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	253 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	254 #elif $functions.func == 'stats':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	255 $functions.freq
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	256 $functions.hardy
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	257 $functions.missing
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	258 $functions.het
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	259 #if $functions.sex.sex_stats:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	260 $functions.sex.sex_stats
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	261 #if $functions.sex.mode:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	262 $functions.sex.mode.mode
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	263 #if $functions.sex.mode.mode == 'ycount'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	264 $functions.sex.mode.female_max
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	265 $functions.sex.mode.male_min
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	266 $functions.sex.mode.female_max_obvs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	267 $functions.sex.mode.male_min_obvs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	268 #elif $functions.sex.mode.mode == 'y-only'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	269 $functions.sex.mode.female_max_obvs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	270 $functions.sex.mode.male_min_obvs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	271 #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	272 $functions.sex.mode.female_max
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	273 $functions.sex.mode.male_min
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	274 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	275 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	276 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	277
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	278
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	279 #elif $functions.func == 'link':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	280 #if $functions.set_indep.choice == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	281 --indep-pairwise $functions.set_indep.window $functions.set_indep.step $functions.set_indep.r2
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	282 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	283 ## #elif $functions.func == 'pair_compare':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	284 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	285 ## #elif $functions.func == 'dist_sim':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	286 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	287 #elif $functions.func == 'stratification':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	288 #if $functions.read_genome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	289 --read-genome $functions.read_genome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	290 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	291 #if $functions.cluster.cluster == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	292 --cluster
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	293 #for $type in $functions.cluster.modifiers
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	294 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	295 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	296 #if $functions.cluster.mds.mds_scaling == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	297 --mds-plot $functions.cluster.mds.dimensions
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	298 #for $type in $functions.cluster.mds.modifiers
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	299 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	300 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	301 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	302 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	303
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	304 #elif $functions.func == 'association':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	305 #if $functions.assoc.assoc == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	306 --assoc
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	307 #if $functions.assoc.perm.perm == 'perm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	308 perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	309 #elif $functions.assoc.perm.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	310 mperm='$functions.assoc.perm.value'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	311 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	312 $functions.assoc.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	313 $functions.assoc.perm_count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	314 $functions.assoc.fisher
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	315 $functions.assoc.count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	316 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	317 #if $functions.adjust.adjust == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	318 --adjust
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	319 #for $type in $functions.adjust.tests:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	320 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	321 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	322 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	323 ## #if $functions.linear.linear == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	324 ## --linear
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	325 ## #if $functions.linear.perm == 'perm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	326 ## perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	327 ## #elif $functions.linear.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	328 ## mperm='$functions.linear.perm.value'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	329 ## #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	330 ## $functions.linear.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	331 ## $functions.linear.perm_count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	332 ## $functions.linear.dominance
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	333 ## $functions.linear.hide_covar
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	334 ## $functions.linear.sex_covar
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	335 ## $functions.linear.interaction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	336 ## $functions.linear.beta
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	337 ## $functions.linear.standard_beta
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	338 ## $functions.linear.intercept
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	339 ## #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	340 #if $functions.logistic.logistic == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	341 --logistic
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	342 #if $functions.logistic.perm.perm == 'perm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	343 perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	344 #elif $functions.logistic.perm.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	345 mperm='$functions.logistic.perm.value'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	346 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	347 $functions.logistic.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	348 $functions.logistic.perm_count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	349 $functions.logistic.dominance
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	350 $functions.logistic.hide_covar
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	351 $functions.logistic.sex_covar
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	352 $functions.logistic.interaction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	353 $functions.logistic.beta
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	354 $functions.logistic.intercept
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	355 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	356
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	357 #elif $functions.func == 'ibd':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	358 #if $functions.genome.output_genome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	359 --genome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	360 #for $type in $functions.genome.modifiers
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	361 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	362 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	363 #if $functions.genome.min:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	364 --min $functions.genome.min
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	365 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	366 #if $functions.genome.max:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	367 --max $functions.genome.max
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	368 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	369 #if $functions.genome.ppc:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	370 --ppc-gap $functions.genome.ppc
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	371 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	372 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	373
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	374 ## #elif $functions.func == 'scoring':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	375 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	376 ## #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	377 ## --rerun $functions.logfile
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	378 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	379 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	380
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	381 --make-bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	382 --out plink_output/plink_output
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	383 ]]></command>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	384 <inputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	385 <section name='inputs' title='Data inputs' expanded='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	386 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	387 <param name='filetype' type='select' label='Main input data type'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	388 <option value='bfile'>plink file</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	389 <option value='vcf'>VCF input file</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	390 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	391 <when value='bfile'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	392 <param format='binary' name='bed' type='data' label='plink bed file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	393 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	394 <param format='txt' name='fam' type='data' label='plink fam file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	395 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	396 <when value='vcf'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	397 <param name='input' format='vcf,bcf' type='data' label='VCF/BCF Input file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	398 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	399 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	400 <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	401 <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	402 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	403 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	404 <param name='func' type='select' label='Plink functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	405 <option value='filtering'>Filtering</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	406 <option value='data_manage'>Data Management</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	407 <option value='stats'>Basic statistics</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	408 <option value='link'>Linkage disequalibrium</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	409 <option value='stratification'>Population stratification</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	410 <option value='association'>Association analysis</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	411 <option value='ibd'>Identity-by-descent</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	412 <!-- <option value='rerun'>Rerun</option> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	413 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	414 <when value='filtering'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	415 <conditional name='id_list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	416 <param name='func' type='select' label='ID list functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	417 <option value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	418 <option value='keep'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	419 <option value='keep-fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	420 <option value='remove'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	421 <option value='remove-fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	422 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	423 <when value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	424 <when value='keep'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	425 <param format='tabular,tsv' name='file' type='data' label='Keep file.' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis;'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	426 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	427 <when value='keep-fam'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	428 <param format='tabular,tsv' name='file' type='data' label='Keep-fam file' help='Accepts text files with family IDs in the first column, and keeps entire families.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	429 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	430 <when value='remove'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	431 <param format='tabular,tsv' name='file' type='data' label='Remove file' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all listed samples from the current analysis'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	432 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	433 <when value='remove-fam'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	434 <param format='tabular,tsv' name='file' type='data' label='Remove-fam file' help='Acceptz text files with family IDs in the first column, and removes entire families.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	435 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	436 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	437 <conditional name='extraction'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	438 <param name='ex_func' type='select' label='ID extraction functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	439 <option value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	440 <option value='extract'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	441 <option value='exclude'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	442 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	443 <when value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	444 <when value='extract'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	445 <param format='txt' name='file' type='data' label='Extract' help='Accepts one or more text file(s) with variant IDs , and removes all unlisted variants from the current analysis'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	446 <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	447 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	448 <when value='exclude'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	449 <param format='txt' name='file' type='data' label='Exclude' help='Accepts one or more text file(s) with variant IDs , and removes all listed variants from the current analysis'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	450 <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	451 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	452 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	453 <!-- <param name='border' type='integer' label='Bed border bp' help='Extends all the intervals in an input BED file (for e.g. extract bed0) by the given number of base-pairs on both sides.' optional='true'/> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	454 <!-- <conditional name='col-cond'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	455 <param name='func' type='select' label='ID list functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	456 <option value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	457 <option value='extract-col-cond'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	458 <option value='extract-col-cond-match'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	459 <option value='extract-col-cond-mismatch'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	460 <option value='extract-col-cond-substr'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	461 <option value='extract-col-cond-min'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	462 <option value='extract-col-cond-max'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	463 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	464 <when value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	465 <when value='extract-col-cond'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	466 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	467 <when value='extract-col-cond-match'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	468 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	469 <when value='extract-col-cond-mismatch'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	470 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	471 <when value='extract-col-cond-substr'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	472 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	473 <when value='extract-col-cond-min'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	474 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	475 <when value='extract-col-cond-max'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	476 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	477 </conditional> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	478 <param name='chromosome' type='text' label='Chromosome(s)' help='Excludes all variants not on the listed chromosome(s). Can be listed as single chromsome, a hyphenated range, or comma separated list.' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	479 <expand macro='chr_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	480 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	481 <param name='excluded_chromosome' type='text' label='Exclude Chromosome(s)' help='Excludes all variants on the listed chromosome(s). Can be listed as single chromsome, a hyphenated range, or comma separated list.' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	482 <expand macro='chr_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	483 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	484 <param name='extra_chromosomes' type='boolean' truevalue='--aec' falsevalue='' checked='false' label='Allow extra chromosomes' help='Allows specified extra chromosomes/scaffolds not normally listed. ex. chr1_gl000191_random.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	485 <param name='autosome' type='select' label='Autosome/unplaced exclusion'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	486 <option value='none'>None</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	487 <option value='--autosome'>Exclude all unplaced and non-autosomal variants</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	488 <option value='--autosome-par'>Excludes all unplaced and non-autosomal variants, but keep XY/PAR1/PAR2. Can be combined with exclude-chromosmes.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	489 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	490 <param name='snps_exclusives' type='select' label='SNP exclusive'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	491 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	492 <option value='--snps-only'>Only return SNPs</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	493 <option value='acgt'>Return SNPs, excluding any other than {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', missing}</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	494 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	495 <conditional name='ranges'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	496 <param name='single_multi' type='select' label='Single or multiple variant-based range window?'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	497 <option value=''>No range specified</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	498 <option value='single'>Single variants</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	499 <option value='multi'>Multiple variants</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	500 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	501 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	502 <when value='single'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	503 <conditional name='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	504 <param name='type' type='select' label='Specify range for variants'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	505 <option value='variant'>Around/between specific variant(s)</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	506 <option value='window'>Around a specific variant</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	507 <option value='range'>Within a specific area (Must also specify a single chromosome in above input)</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	508 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	509 <when value='variant'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	510 <param name='from' type='text' label='From' help='Variant ID. Excludes all variants on different chromosomes than the named variant, as well as those with smaller base-pair position values. If they are used together but the --from variant is after the --to variant, they are automatically swapped.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	511 <param name='to' type='text' label='To' help='Variant ID. Excludes all variants on different chromosomes than the named variant, as well as those with larger base-pair position values. If they are used together but the --from variant is after the --to variant, they are automatically swapped.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	512 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	513 <when value='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	514 <param name='snp' type='text' label='SNP variant id to include' help='Use this OR SNP variant to exclude' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	515 <expand macro='snp_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	516 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	517 <param name='exclude_snp' type='text' label='SNP variant id to exclude' help='Use this OR SNP variant to include' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	518 <expand macro='snp_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	519 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	520 <param name='window' type='integer' label='Window' help='All variants with physical position no more than half the specified kb distance (decimal permitted) from the named variant are loaded as well' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	521 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	522 <when value='range'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	523 <param name='from_bp' type='integer' label='from-bp' help='These flags let you use physical positions to specify a variant range to load. Must also have specified a chromosome in above settings.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	524 <param name='to_bp' type='integer' label='to-bp' help='These flags let you use physical positions to specify a variant range to load. Must also have specified a chromosome in above settings.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	525 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	526 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	527 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	528 <when value='multi'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	529 <param name='force_intersect' type='boolean' truevalue='--force-intersect' falsevalue='' label='Force intersect' help='To reduce the potential for confusion, PLINK 2 normally errors out when multiple variant-inclusion filters
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	530 (--extract[-intersect], --extract-col-cond, --from/--to, --from-bp/--to-bp, --snp, --snps) are specified, since it may not be obvious whether the intersection or union will be taken.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	531 --force-intersect allows the run to proceed; the set intersection will be taken.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	532 <param name='snps' type='text' label='List of SNP variant ids to include' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	533 <expand macro='snp_space_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	534 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	535 <param name='exclude_snps' type='text' label='List of SNP variant ids to exclude' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	536 <expand macro='snp_space_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	537 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	538 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	539 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	540 <conditional name='thinning'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	541 <param name='thinning' type='select' label='Arbitrary thinning'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	542 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	543 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	544 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	545 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	546 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	547 <param name='thin' type='float' label='Thin' min='0' max='1.0' help='Removes variants at random by retaining each variant with probability p' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	548 <param name='thin_count' type='integer' label='Thin Count' help='Removes variants at random until only n remain' min='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	549 <param name='bp_space' type='integer' label='BP space' help='Excludes one variant from each pair closer than the given bp count' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	550 <param name='thin_indiv' type='float' label='Thin Individual' min='0' max='1.0' help='Removes samples at random by retaining each sample with probability p' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	551 <param name='thin_indiv_count' type='integer' label='Thin Individual count' min='1' help='Removes samples at random until only n remain.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	552 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	553 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	554 <!-- <conditional name='pheno_cov_based'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	555 <param name='pheno_cov' type='select' label='Phenotype/Covariate-based'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	556 <option value='No' selected='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	557 <option value='phenotype'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	558 <option value='Covariate'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	559 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	560 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	561 <when value='phenotype'> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	562 <!-- keep-if <phenotype/covariate name> <operator> <value>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	563 remove-if <phenotype/covariate name> <operator> <value>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	564 require-pheno [phenotype name(s)...]
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	565 keep-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	566 keep-cat-names <name(s)...>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	567 remove-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	568 remove-cat-names <name(s)...>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	569 keep-cat-pheno <phenotype/covariate name>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	570 remove-cat-pheno <phenotype/covariate name>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	571 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	572 <when value='Covariate'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	573 keep-if <phenotype/covariate name> <operator> <value>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	574 remove-if <phenotype/covariate name> <operator> <value>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	575 require-covar [covariate name(s)...]
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	576 keep-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	577 keep-cat-names <name(s)...>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	578 remove-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	579 remove-cat-names <name(s)...>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	580 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	581 </conditional> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	582 <section name='geno_rates' title='Missing Genotype Rates' expanded='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	583 <param name='geno' type='float' min='0' max='1' label='Set Geno' help='filters out all variants with missing call rates exceeding the provided value (default 0.1) to be removed' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	584 <param name='mind' type='float' min='0' max='1' label='Set Mind' help='filters out all samples with missing call rates exceeding the provided value (default 0.1) to be removed' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	585 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	586 <section name='allele_freq' title='Allele Frequencies' expanded='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	587 <param name='maf' type='float' label='Minimum allele frequency' min='0' max='1.0' help='Filters out all variants with allele frequency below the provided threshold' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	588 <param name='max_maf' type='float' label='Maximum allele frequency' min='0' max='1.0' help='Filters out all variants with allele frequency above the provided threshold' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	589 <param name='mac' type='integer' label='Minimum allele count' min='1' help='Filters out all variants with allele counts below the provided threshold' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	590 <param name='max_mac' type='integer' label='Maximum allele count' min='0' help='filters out all variants with allele counts above the provided threshold' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	591 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	592 <conditional name='hwe'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	593 <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	594 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	595 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	596 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	597 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	598 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	599 <param name='hwe_val' type='float' label='Hardy-Weinberg Equilibrium' help='Filters out all variants which have Hardy-Weinberg equilibrium exact test
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	600 p-value below the provided threshold. It is recommended setting a low threshold—serious genotyping errors often yield extreme p-values like 1e-501 which
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	601 are detected by any reasonable configuration of this test, while genuine SNP-trait associations can be expected to deviate slightly from Hardy-Weinberg
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	602 equilibrium (so it is dangerous to choose a threshold that filters out too many variants).' value='1e-50' min='0' max='1'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	603 <param name='modifiers' type='select' label='Test modifiers' multiple='true' display='checkboxes' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	604 <option value='midp'>Apply the mid-p adjustment described in Graffelman J, Moreno V (2013) The mid p-value in exact tests for Hardy-Weinberg equilibrium</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	605 <option value='include-nonctrl'>Don't ignore cases and missing phenotypes'</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	606 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	607 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	608 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	609 <conditional name='sex_founder_filter'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	610 <param name='filter' type='select' label='Filter on sex and/or founders'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	611 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	612 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	613 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	614 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	615 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	616 <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	617 <option value='--filter-cases'>Only include cases</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	618 <option value='--filter-controls'>Only include controls</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	619 <option value='--filter-males'>Only include males</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	620 <option value='--filter-females'>Only include females</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	621 <option value='--filter-founders'>Exclude all samples with at least one known parental ID</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	622 <option value='--filter-nonfounders'>Only include samples with at least one known parental ID</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	623 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	624 <param name='no_sex_select' type='select' label='No sex settings' optional='true' help='How to deal with ambiguous sex phenotypes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	625 <option value='--allow-no-sex'>Prevent samples with ambiguous sex frim having their phenotypes set to missing when analysis commands are run</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	626 <option value='--must-have-sex'>Force phenotypes of ambiguous-sex samples to missing in output</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	627 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	628 <param name='nonfounders' type='boolean' label='Nonfouders' truevalue='--nonfounders' falsevalue='' checked='false' help='Include nonfounders in --freq[x] or --maf/--max-maf/--hwe calculations'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	629 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	630 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	631 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	632 <when value='data_manage'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	633 <conditional name='bmerge'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	634 <param name='set' type='select' label='Merge plink tilesets'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	635 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	636 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	637 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	638 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	639 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	640 <param format='binary' name='bed' type='data' label='plink bed file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	641 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	642 <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	643 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	644 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	645 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	646 <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	647 <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	648 <expand macro='template_sanitizer'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	649 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	650 <param name='length' type='integer' label='Max allele length' help='Length threshold to rename alleles. Recommended default is 23' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	651 <conditional name='update_cols'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	652 <param name='set' type='select' label='Update variant columns'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	653 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	654 <option value='update_map'>update-map</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	655 <option value='update_name'>update-name</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	656 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	657 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	658 <when value='update_map'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	659 <param name='input' type='data' format='tabular,tsv' help='By default, the new value is read from column 2 and the (old) variant ID from column 1, but you can adjust these positions with the second and third parameters.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	660 <param name='col_num' type='integer' min='0' label='New ID column number' value='2'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	661 <param name='old_col' type='integer' min='0' label='Old ID column' value='1'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	662 <param name='skip' type='text' label='Skip' optional='true' help='Either a nonnegative integer, in which case it indicates the number of lines to skip at the top of the file, or a single nonnumeric character, which causes each line with that leading character to be skipped.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	663 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	664 <when value='update_name'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	665 <param name='input' type='data' format='tabular,tsv' help='By default, the new value is read from column 2 and the (old) variant ID from column 1, but you can adjust these positions with the second and third parameters.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	666 <param name='col_num' type='integer' min='0' label='BP column number' value='2'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	667 <param name='var_col' type='integer' min='0' label='Variant ID column' value='1'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	668 <param name='skip' type='text' label='Skip' optional='true' help='Either a nonnegative integer, in which case it indicates the number of lines to skip at the top of the file, or a single nonnumeric character, which causes each line with that leading character to be skipped.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	669 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	670 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	671 <conditional name='ref_allele'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	672 <param name='set' type='select' label='Set REF alleles' help='These cannot be used with any other commands.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	673 <option value='no'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	674 <option value='yes'>Yes</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	675 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	676 <when value='no'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	677 <when value='yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	678 <param name='file' type='data' format='vcf' label='Set all alleles specified in the file to REF'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	679 <param name='column' type='integer' optional='true' min='1' label='Reference column number'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	680 <param name='var_id' type='integer' optional='true' min='1' label='Variant id column in file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	681 <param name='skip' label='Skip' type='text' help='Either a nonnegative integer, in which case it indicates the number of lines to skip at the top of the file, or a single nonnumeric character, which causes each line with that leading character to be skipped.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	682 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	683 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	684 <conditional name='a2_allele'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	685 <param name='set' type='select' label='Set a2 alleles' help='These cannot be used with any other commands.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	686 <option value='no'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	687 <option value='yes'>Yes</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	688 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	689 <when value='no'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	690 <when value='yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	691 <param name='file' type='data' format='vcf' label='Set all alleles specified in the file to first ALT allele'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	692 <param name='column' type='integer' value='4' optional='true' label='Alt column number'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	693 <param name='var_id' type='integer' value='3' optional='true' label='Variant id column in file'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	694 <param name='skip' label='Skip' type='boolean' truevalue='skip' falsevalue='' checked='false' help='Either a nonnegative integer, in which case it indicates the number of lines to skip at the top of the file, or a single nonnumeric character, which causes each line with that leading character to be skipped.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	695 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	696 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	697 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	698 <when value='stats'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	699 <param name='freq' label='Return allele frequency file' type='boolean' truevalue='--freq' falsevalue=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	700 <param name='hardy' label='Return Hardy-Weinberg statistics file' type='boolean' truevalue='--hardy' falsevalue='' help='Writes out writes autosomal Hardy-Weinberg equilibrium exact test statistics'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	701 <param name='missing' label='Missing Data' type='boolean' truevalue='--missing' falsevalue='' help='produces sample-based and variant-based missing data reports'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	702 <param name='het' label='Inbreeding' type='boolean' truevalue='--het' falsevalue='' help='Compute observed and expected homozygous/heterozygous genotype counts for each sample, and reports method-of-moments F coefficient estimates'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	703 <conditional name='sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	704 <param name='sex_stats' label='Sex imputation' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	705 <option value=''>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	706 <option value='--check-sex'>Compare sex assignments in input dataset with those imputed from X chromosome inbreeding coefficients</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	707 <option value='--impute-sex'> Changes sex assignments to the imputed values. Cannot be set with any other flags.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	708 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	709 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	710 <when value='--check-sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	711 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	712 <param name='mode' type='select' label='Mode select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	713 <option value=''>Base</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	714 <option value='ycount'>ycount</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	715 <option value='y-only'>y-only</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	716 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	717 <when value=''>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	718 <param name='female_max' type='float' label='Female max proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	719 <param name='male_min' type='float' label='Male min proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	720 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	721 <when value='ycount'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	722 <param name='female_max' type='float' label='Female max proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	723 <param name='male_min' type='float' label='Male min proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	724 <param name='female_max_obvs' type='integer' label='Female max count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	725 <param name='male_min_obvs' type='integer' label='Male min count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	726 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	727 <when value='y-only'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	728 <param name='female_max_obvs' type='integer' label='Female max count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	729 <param name='male_min_obvs' type='integer' label='Male mincountn' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	730 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	731 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	732 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	733 <when value='--impute-sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	734 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	735 <param name='mode' type='select' label='Mode select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	736 <option value=''>Base</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	737 <option value='ycount'>ycount</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	738 <option value='y-only'>y-only</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	739 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	740 <when value=''>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	741 <param name='female_max' type='float' label='Female max proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	742 <param name='male_min' type='float' label='Male min proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	743 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	744 <when value='ycount'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	745 <param name='female_max' type='float' label='Female max proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	746 <param name='male_min' type='float' label='Male min proportion' min='0' max='1' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	747 <param name='female_max_obvs' type='integer' label='Female max count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	748 <param name='male_min_obvs' type='integer' label='Male min count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	749 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	750 <when value='y-only'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	751 <param name='female_max_obvs' type='integer' label='Female max count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	752 <param name='male_min_obvs' type='integer' label='Male min count' min='0' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	753 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	754 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	755 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	756 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	757 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	758 <when value='link'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	759 <conditional name='set_indep'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	760 <param name='choice' label='Variant pruning' type='select' help='Since two-variant r2 only makes sense for biallelic variants, these collapse multiallelic variants down to most common allele vs. the rest.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	761 <option value='Yes'>Yes</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	762 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	763 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	764 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	765 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	766 <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	767 <param name='step' type='integer' label='Step size (variant ct)' value='5'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	768 <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	769 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	770 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	771
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	772 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	773 <when value='stratification'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	774 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	775 <conditional name='cluster'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	776 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	777 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	778 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	779 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	780 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	781 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	782 <param name='modifiers' type='select' label='Cluster flag modifiers' multiple='true' display='checkboxes' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	783 <option value='cc'>Prevent two all-case or two all-control clusters from being merged.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	784 <option value='group-avg'>By default, the distance between two clusters is defined as the maximum pairwise distance between a member of the first cluster and a member of the second cluster. Cause average pairwise distance to be used instead.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	785 <option value='missing'>Cause clustering to be based on identity-by-missingness</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	786 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	787 <conditional name='mds'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	788 <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	789 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	790 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	791 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	792 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	793 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	794 <param name='dimensions' type='integer' label='Dimension count' value='10'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	795 <param name='modifiers' type='select' label='mds-plot flag modifiers' multiple='true' display='checkboxes' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	796 <option value='by-cluster'>Perform mds scaling on an inter-cluster distance matrix</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	797 <option value='eigendecomp'>Request faster eigendocomposition-based algorithm, yielding slightly different results</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	798 <option value='eigvals'>Write out top eigenvalues to separate file</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	799 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	800 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	801 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	802 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	803 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	804 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	805 <when value='association'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	806 <conditional name='assoc'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	807 <param name='assoc' label='Perform 1df chi-square allelic test' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	808 <option value=''>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	809 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	810 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	811 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	812 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	813 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	814 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	815 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	816 <option value='perm'>Perform Monte Carlo permutation test</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	817 <option value='mperm'>Perform a max(T) permutation test with specified number of replications</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	818 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	819 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	820 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	821 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	822 <param name='value' label='Replications' type='integer' min='0' value='10000'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	823 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	824 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	825 <param name='genedrop' label='genedrop' type='boolean' truevalue='genedrop' falsevalue='' checked='false' help='Cause offspring genotypes to be regenerated via gene-dropping in the permutation test.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	826 <param name='perm_count' label='Perm-count' type='boolean' truevalue='perm-count' falsevalue='' checked='false' help='Cause the permutation test report to include permutation counts instead of frequencies.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	827 <param name='fisher' label='Fisher tests' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	828 <option value=''>Don't specify</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	829 <option value='fisher'>Use fisher's exact test</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	830 <option value='fisher-midp'>User Fisher's exact test with Lancaster's mid-p adjustment</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	831 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	832 <param name='count' label='Counts' type='boolean' truevalue='counts' falsevalue='' checked='false' help='Report allele counts instead of frequencies'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	833 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	834 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	835 <conditional name='adjust'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	836 <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	837 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	838 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	839 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	840 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	841 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	842 <param name='tests' label='Testing modifiers' type='select' multiple='true' display='checkboxes' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	843 <option value='gc'>Use genomic-controlled p-values in the formulas</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	844 <option value='log10'>Replace the p-values in the .adjusted file with their negative base 10 logarithms.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	845 <option value='qq-plot'>Add a quantile column to simplify QQ plotting.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	846 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	847 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	848 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	849 <!-- <conditional name='linear'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	850 <param name='linear' type='select' label='Perform linenar regression and return report'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	851 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	852 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	853 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	854 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	855 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	856 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	857 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	858 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	859 <option value='perm'>Perform Monte Carlo permutation test</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	860 <option value='mperm'>Perform a max(T) permutation test with specified number of replications</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	861 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	862 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	863 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	864 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	865 <param name='value' label='Replications' type='integer' min='0' value='10000'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	866 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	867 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	868 <param name='genedrop' label='genedrop' type='boolean' truevalue='genedrop' falsevalue='' checked='false' help='Cause offspring genotypes to be regenerated via gene-dropping in the permutation test.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	869 <param name='perm_count' label='Perm-count' type='boolean' truevalue='perm-count' falsevalue='' checked='false' help='Cause the permutation test report to include permutation counts instead of frequencies.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	870 <param name='set_test' label='set_test' type='boolean' truevalue='set-test' falsevalue='' checked='false' help='Test the significance of variant sets'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	871 <param name='dominance' label='Set dominance model' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	872 <option value=''>Don't specify</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	873 <option value='genotypic'>Add an additive effect/dominance deviation 2df joint test (with two genotype-dependent variables in the regression, one with 0/1/2 coding and the second with 0/1/0</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	874 <option value='hethom'>Add an additive effect/dominance deviation 2df joint test (with two genotype-dependent variables in the regression, one with 0/0/1 coding and the second with 0/1/0</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	875 <option value='dominant'>Assume full dominance in A1 allele</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	876 <option value='recessive'>Assume full recessiveness in A1 allele</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	877 <option value='no-snp'>Request a regression only on the phenotype and the covariates, without reference to genomic data</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	878 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	879 <param name='hide_covar' label='hide_covar' type='boolean' truevalue='hide-covar' falsevalue='' checked='false' help='Remove covariate-specific lines from the main report'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	880 <param name='sex_covar' label='Sex as a covariate' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	881 <option value=''>Only used where specified</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	882 <option value='sex'>By default, when at least one male and one female is present, sex (male = 1, female = 0) is automatically added as a covariate on X chromosome SNPs, and nowhere else. The 'sex' modifier causes it to be added everywhere.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	883 <option value='no-x-sex'>By default, when at least one male and one female is present, sex (male = 1, female = 0) is automatically added as a covariate on X chromosome SNPs, and nowhere else. The 'no-x-sex' modifier causes it to be excluded everywhere</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	884 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	885 <param name='interaction' label='interaction' type='boolean' truevalue='interaction' falsevalue='' checked='false' help='Add genotype x covariate interactions to the model.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	886 <param name='beta' label='beta' type='boolean' truevalue='beta' falsevalue='' checked='false' help=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	887 <param name='standard_beta' label='standard-beta' type='boolean' truevalue='standard-beta' falsevalue='' checked='false' help=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	888 <param name='intercept' label='intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	889 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	890 </conditional> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	891 <conditional name='logistic'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	892 <param name='logistic' type='select' label='Perform logistic regression and return report'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	893 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	894 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	895 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	896 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	897 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	898 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	899 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	900 <option value='No'>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	901 <option value='perm'>Perform Monte Carlo permutation test</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	902 <option value='mperm'>Perform a max(T) permutation test with specified number of replications</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	903 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	904 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	905 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	906 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	907 <param name='value' label='Replications' type='integer' min='0' value='10000'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	908 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	909 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	910 <param name='genedrop' label='genedrop' type='boolean' truevalue='genedrop' falsevalue='' checked='false' help='Cause offspring genotypes to be regenerated via gene-dropping in the permutation test.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	911 <param name='perm_count' label='Perm-count' type='boolean' truevalue='perm-count' falsevalue='' checked='false' help='Cause the permutation test report to include permutation counts instead of frequencies.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	912 <param name='dominance' label='Set dominance model' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	913 <option value=''>Don't specify</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	914 <option value='genotypic'>Add an additive effect/dominance deviation 2df joint test (with two genotype-dependent variables in the regression, one with 0/1/2 coding and the second with 0/1/0</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	915 <option value='hethom'>Add an additive effect/dominance deviation 2df joint test (with two genotype-dependent variables in the regression, one with 0/0/1 coding and the second with 0/1/0</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	916 <option value='dominant'>Assume full dominance in A1 allele</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	917 <option value='recessive'>Assume full recessiveness in A1 allele</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	918 <option value='no-snp'>Request a regression only on the phenotype and the covariates, without reference to genomic data</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	919 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	920 <param name='hide_covar' label='Hide covar' type='boolean' truevalue='hide-covar' falsevalue='' checked='false' help='Remove covariate-specific lines from the main report'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	921 <param name='sex_covar' label='Sex as a covariate' type='select'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	922 <option value=''>Only used where specified</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	923 <option value='sex'>By default, when at least one male and one female is present, sex (male = 1, female = 0) is automatically added as a covariate on X chromosome SNPs, and nowhere else. The 'sex' modifier causes it to be added everywhere.</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	924 <option value='no-x-sex'>By default, when at least one male and one female is present, sex (male = 1, female = 0) is automatically added as a covariate on X chromosome SNPs, and nowhere else. The 'no-x-sex' modifier causes it to be excluded everywhere</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	925 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	926 <param name='interaction' label='Interaction' type='boolean' truevalue='interaction' falsevalue='' checked='false' help='Add genotype x covariate interactions to the model.'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	927 <param name='beta' label='Beta' type='boolean' truevalue='beta' falsevalue='' checked='false' help=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	928 <param name='intercept' label='Intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	929 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	930 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	931 <param name='lambda' type='float' label='Lambda value' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	932 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	933 <!-- <when value='scoring'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	934 </when> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	935 <when value='ibd'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	936 <conditional name='genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	937 <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	938 <option value=''>No</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	939 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	940 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	941 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	942 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	943 <param name='min' type='float' label='min' min='0' max='1.0' help='Minimum PI_HAT value' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	944 <param name='max' type='float' label='max' min='0' max='1.0' help='Maximum PI_HAT value' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	945 <param name='ppc' type='integer' label='PPC-gap' min='0' help='Minimum distance between informative pairs of SNPs used in the pairwise population concordance (PPC) inn kbs' value='500' optional='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	946 <param name='modifiers' type='select' label='Genome flag modifiers' multiple='true' display='checkboxes' optional='true'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	947 <option value='rel-check'>Remove pairs of samples with different FIDs</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	948 <option value='full'>Add IBS , HOMHOM and HETHET fields to output</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	949 <option value='unbounded'>Turn off clipping due to IBD estimator</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	950 <option value='nudge'>If PI_HAT2 greater than P(IBD=2), adjusts the final estimates to P(IBD=0) := (1-p2), P(IBD=1) := 2p(1-p), and P(IBD=2) := p2, where p is the current PI_HAT</option>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	951 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	952 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	953 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	954 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	955 <!-- <when value='rerun'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	956 <param type='data' name='logfile' format='binary' label='Plink Log File'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	957 </when> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	958 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	959 </inputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	960 <outputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	961 <!--Main-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	962 <collection name='plink_out' type='list' label='Plink main outputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	963 <data name='plink_bed' format='binary' from_work_dir='plink_output/plink_output.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	964 <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	965 <data name='plink_fam' format='tabular' from_work_dir='plink_output/plink_output.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	966 <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	967 </collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	968
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	969 <!--Data Manage-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	970 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	971 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	972 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	973 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	974 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	975 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	976
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	977 <!--Stats-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	978 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	979 <filter>functions['func'] == 'stats' and functions['freq']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	980 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	981 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	982 <filter>functions['func'] == 'stats' and functions['hardy']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	983 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	984 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	985 <filter>functions['func'] == 'stats' and functions['missing']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	986 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	987 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	988 <filter>functions['func'] == 'stats' and functions['missing']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	989 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	990 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	991 <filter>functions['func'] == 'stats' and functions['het']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	992 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	993 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	994 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	995 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	996
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	997 <!--Association-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	998 <!--assoc-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	999 <data name='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1000 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1001 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1002 <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1003 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1004 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1005 <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association Max(T) permutation test'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1006 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and not functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1007 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1008 <data name='fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher' label='${tool.name}: Association Fisher'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1009 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1010 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1011 <data name='fisher_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.perm' label='${tool.name}: Association Fisher perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1012 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1013 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1014 <data name='fisher_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.mperm' label='${tool.name}: Association Fisher mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1015 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1016 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1017
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1018 <!--adjust-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1019 <data name='adjust' format='tabular' from_work_dir='plink_output/plink_output.assoc.adjusted' label='${tool.name}: Adjusted'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1020 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and not functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1021 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1022 <data name='adjust_fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.adjusted' label='${tool.name}: Fisher Adjusted'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1023 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and functions['assoc']['fisher']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1024 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1025 <data name='adjust_logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.adjusted' label='${tool.name}: Logistic Adjusted'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1026 <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes' and functions['logistic']['logistic'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1027 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1028
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1029 <!-- <data name='linear' format='tabular' from_work_dir='plink_output/plink_output.assoc.linenar' label='${tool.name}: Linear Regression'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1030 <filter>functions['func'] == 'association' and functions.func.association.linear['linear'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1031 </data> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1032
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1033 <!--Logistic-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1034 <data name='logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic' label='${tool.name}: Logistic Regression'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1035 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1036 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1037 <data name='logistic_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.perm' label='${tool.name}: Logistic Association Monte Carlo'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1038 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'perm'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1039 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1040 <data name='logistic_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.mperm' label='${tool.name}: Logistic Association Max(T) permutation test'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1041 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'mperm'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1042 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1043
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1044 <!--Link-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1045 <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1046 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1047 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1048 <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1049 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1050 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1051
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1052 <!--IBD-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1053 <data name='genome' format='tabular' from_work_dir='plink_output/plink_output.genome' label='${tool.name}: Genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1054 <filter>functions['func'] == 'ibd' and functions['genome']['output_genome']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1055 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1056
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1057 <!--Stratifiction-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1058 <data name='mds' format='txt' from_work_dir='plink_output/plink_output.mds' label='${tool.name}: MDS'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1059 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1060 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1061 <data name='cluster1' format='tabular' from_work_dir='plink_output/plink_output.cluster1' label='${tool.name}: Cluster 1'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1062 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1063 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1064 <data name='cluster2' format='tabular' from_work_dir='plink_output/plink_output.cluster2' label='${tool.name}: Cluster 2'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1065 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1066 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1067 <data name='cluster3' format='tabular' from_work_dir='plink_output/plink_output.cluster3' label='${tool.name}: Cluster 3'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1068 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and 'missing' not in functions['cluster']['modifiers']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1069 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1070 <data name='cluster3missing' format='tabular' from_work_dir='plink_output/plink_output.cluster3.missing' label='${tool.name}: Cluster 3 missing'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1071 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['modifiers'] and 'missing' in functions['cluster']['modifiers']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1072 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1073 <data name='mds_miss' format='tabular' from_work_dir='plink_output/plink_output.mdist.missing' label='${tool.name}: Mdist missing'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1074 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['modifiers'] and 'missing' in functions['cluster']['modifiers']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1075 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1076 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1077 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1078 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1079 </outputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1080 <tests>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1081 <test expect_num_outputs='5'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1082 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1083 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1084 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1085 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1086 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1087 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1088 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1089 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1090 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1091 <param name='func' value='filtering'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1092 <conditional name='id_list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1093 <param name='func' value='remove'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1094 <param name='file' value='1.tabular'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1095 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1096 <conditional name='extraction'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1097 <param name='ex_func' value='exclude'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1098 <param name='file' value='testing.txt'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1099 <param name='range' value='true'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1100 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1101 <param name='snps_exclusives' value='--snps-only'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1102 <conditional name='ranges'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1103 <param name='single_multi' value='single'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1104 <conditional name='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1105 <param name='type' value='variant'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1106 <param name='from' value='snp0'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1107 <param name='to' value='snp3'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1108 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1109 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1110 <conditional name='thinning'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1111 <param name='thinning' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1112 <param name='thin_count' value='4'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1113 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1114 <section name='geno_rates'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1115 <param name='geno' value='0.02'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1116 <param name='mind' value='0.02'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1117 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1118 <section name='allele_freq'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1119 <param name='maf' value='0.01'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1120 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1121 <conditional name='hwe'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1122 <param name='hwe' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1123 <param name='hwe_val' value='1e-50'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1124 <param name='modifiers' value='midp,include-nonctrl'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1125 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1126 <conditional name='sex_founder_filter'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1127 <param name='filter' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1128 <param name='sex_select' value='--filter-cases'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1129 <param name='no_sex_select' value='--allow-no-sex'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1130 <param name='nonfounders' value='--nonfounders'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1131 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1132 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1133 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1134 <element name='plink_bed' file='test1_out.bed' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1135 <element name='plink_bim' file='test1_out.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1136 <element name='plink_fam' file='test1_out.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1137 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1138 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1139
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1140 <test expect_num_outputs='7'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1141 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1142 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1143 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1144 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1145 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1146 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1147 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1148 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1149 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1150 <param name='func' value='data_manage'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1151 <conditional name='bmerge'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1152 <param name='set' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1153 <param name='bed' value='plink_2.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1154 <param name='bim' value='plink_2.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1155 <param name='fam' value='plink_2.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1156 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1157 <param name='recode' value='--recode'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1158 <param name='template' value='@asd#123'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1159 <param name='length' value='23'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1160 <conditional name='update_cols'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1161 <param name='set' value='update_name'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1162 <param name='input' value='update_cols.txt'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1163 <param name='col_num' value='1'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1164 <param name='var_col' value='2'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1165 <param name='skip' value='a'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1166 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1167 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1168 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1169 <element name='plink_bed' file='test2_out.bed' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1170 <element name='plink_bim' file='test2_out.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1171 <element name='plink_fam' file='test2_out.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1172 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1173 <output name='plink_ped' file='out.ped'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1174 <output name='plink_map' file='out.map'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1175 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1176
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1177 <test expect_num_outputs='5'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1178 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1179 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1180 <param name='filetype' value='vcf'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1181 <param name='input' value='test.vcf'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1182 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1183 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1184 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1185 <element name='plink_bed' file='vcf_out.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1186 <element name='plink_bim' file='vcf_out.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1187 <element name='plink_fam' file='vcf_out.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1188 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1189 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1190
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1191 <test expect_num_outputs='11'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1192 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1193 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1194 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1195 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1196 <param name='bim' value='x_plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1197 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1198 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1199 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1200 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1201 <param name='func' value='stats'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1202 <param name='freq' value='--freq'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1203 <param name='hardy' value='--hardy'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1204 <param name='missing' value='--missing'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1205 <param name='het' value='--het'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1206 <conditional name='sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1207 <param name='sex_stats' value='--check-sex'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1208 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1209 <param name='mode' value='ycount'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1210 <param name='female_max' value='0.2'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1211 <param name='male_min' value='0.8'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1212 <param name='female_max_obvs' value='10'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1213 <param name='male_min_obvs' value='200'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1214 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1215 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1216 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1217 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1218 <element name='plink_bed' file='stats.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1219 <element name='plink_bim' file='stats.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1220 <element name='plink_fam' file='stats.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1221 <element name='plink_fam' file='stats.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1222 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1223 <output name='frequency' file='out.freq'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1224 <output name='hardy_out' file='out.hardy'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1225 <output name='missing_1' file='out.imiss'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1226 <output name='missing_2' file='out.lmiss'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1227 <output name='het' file='out.het'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1228 <output name='sex_check' file='out.sexcheck'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1229 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1230
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1231 <test expect_num_outputs='7'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1232 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1233 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1234 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1235 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1236 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1237 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1238 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1239 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1240 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1241 <param name='func' value='link'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1242 <conditional name='set_indep'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1243 <param name='choice' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1244 <param name='window' value='51'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1245 <param name='step' value='6'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1246 <param name='r2' value='0.3'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1247 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1248 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1249 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1250 <element name='plink_bed' file='test5_out.bed' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1251 <element name='plink_bim' file='test5_out.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1252 <element name='plink_fam' file='test5_out.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1253 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1254 <output name='prune_in' file='plink.prune.in'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1255 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1256
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1257 <test expect_num_outputs='10'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1258 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1259 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1260 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1261 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1262 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1263 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1264 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1265 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1266 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1267 <param name='func' value='stratification'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1268 <param name='read_genome' value='plink.genome'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1269 <conditional name='cluster'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1270 <param name='cluster' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1271 <param name='modifiers' value='cc,group-avg'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1272 <conditional name='mds'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1273 <param name='mds_scaling' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1274 <param name='dimensions' value='10'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1275 <param name='modifiers' value='eigendecomp,eigvals'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1276 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1277 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1278 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1279 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1280 <element name='plink_bed' file='test6_out.bed' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1281 <element name='plink_bim' file='test6_out.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1282 <element name='plink_fam' file='test6_out.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1283 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1284 <output name='mds' value='plink.mds' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1285 <output name='cluster1' value='plink.cluster1' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1286 <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1287 <output name='cluster3' value='plink.cluster3' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1288 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1289 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1290
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1291 <test expect_num_outputs='11'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1292 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1293 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1294 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1295 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1296 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1297 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1298 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1299 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1300 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1301 <param name='func' value='association'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1302 <conditional name='assoc'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1303 <param name='assoc' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1304 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1305 <param name='perm' value='mperm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1306 <param name='value' value='10000'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1307 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1308 <param name='fisher' value='fisher-midp'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1309 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1310 <conditional name='adjust'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1311 <param name='adjust' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1312 <param name='tests' value='gc,log10,qq-plot'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1313 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1314 <conditional name='logistic'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1315 <param name='logistic' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1316 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1317 <param name='perm' value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1318 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1319 <param name='genedrop' value='genedrop'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1320 <param name='perm_count' value='perm-count'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1321 <param name='dominance' value='dominant'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1322 <param name='hide_covar' value='hide-covar'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1323 <param name='beta' value='beta'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1324 <param name='intercept' value='intercept'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1325 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1326 <param name='lambda' value='1.0'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1327 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1328 <output_collection name='plink_out' type='list'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1329 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1330 <element name='plink_bim' file='out.assoc.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1331 <element name='plink_fam' file='out.assoc.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1332 </output_collection>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1333 <output name='fisher' value="out.assoc.fisher"/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1334 <output name='adjust_fisher' value="out.assoc.fisher.adjusted" sort="True" />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1335 <output name='fisher_mperm' value="out.assoc.fisher.mperm" compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1336 <output name='logistic' value="out.assoc.logistic"/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1337 <output name='adjust_logistic' value="out.assoc.logistic.adjusted"/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1338 <output name='logistic_perm' value="out.assoc.logistic.perm" compare='sim_size'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1339 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1340
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1341 <test expect_num_outputs='6'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1342 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1343 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1344 <param name='filetype' value='bfile'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1345 <param name='bed' value='plink.bed'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1346 <param name='bim' value='plink.bim'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1347 <param name='fam' value='plink.fam'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1348 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1349 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1350 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1351 <param name='func' value='ibd'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1352 <conditional name='genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1353 <param name='output_genome' value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1354 <param name='min' value='0.1'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1355 <param name='max' value='0.9'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1356 <param name='modifiers' value='full,unbounded,nudge'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1357 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1358 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1359 <output name='genome' file='out.genome'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1360 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1361 </tests>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1362 <help><![CDATA[
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1363 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1364
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1365 For detailed usage notes, visit http://www.cog-genomics.org/plink/2.0/
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1366 ]]></help>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1367 <citations>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1368 <citation type='doi'>10.1186/s13742-015-0047-8</citation>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1369 </citations>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b" iuc parents: diff changeset	1370 </tool>

Mercurial > repos > iuc > plink

annotate plink.xml @ 1:b8e3d957c0f5 draft