Mercurial > repos > iuc > plink

annotate plink.xml @ 9:272aca44b3dd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
author iuc
date Sun, 19 Dec 2021 15:53:35 +0000
parents 16d22eee0fe3
children 2c0ac05fe240
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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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
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2 <macros>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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3 <token name='@TOOL_VERSION@'>1.90b6.21</token>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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4 <token name='@VERSION_SUFFIX@'>0</token>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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5 <xml name='template_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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6 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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7 <valid initial='default'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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8 <add value='#' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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9 <add value='@' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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10 <add value='$'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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11 <add value='['/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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12 <add value=']'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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13 <add value='\'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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14 <remove value='&#34;'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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15 <remove value='&#39;'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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16 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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17 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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18 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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19 <xml name='chr_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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20 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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21 <valid initial='string.digits'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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22 <add value='X' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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23 <add value='Y' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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24 <add value=' ' />
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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25 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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26 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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27 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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28 <xml name='snp_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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29 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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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
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31 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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32 </xml>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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33 <xml name='snp_space_sanitizer'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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34 <sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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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
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36 <add value=' '/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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37 </valid>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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38 </sanitizer>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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39 </xml>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
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40 <xml name="log_out_assert">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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41 <output name="plink_log">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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42 <assert_contents>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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43 <has_text text="End time:"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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44 </assert_contents>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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45 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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46 </xml>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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47 </macros>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
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48 <xrefs>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
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49 <xref type="bio.tools">plink</xref>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
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50 </xrefs>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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51 <requirements>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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52 <requirement type='package' version='@TOOL_VERSION@'>plink</requirement>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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53 </requirements>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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54 <command detect_errors='exit_code'><![CDATA[
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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55
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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56 ## Create Plink folder for any inputs
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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57 mkdir ./plink_output
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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58 && mkdir ./plink_input
5
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
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59
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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60
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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61 ## 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
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62 #if $functions.func == 'data_manage':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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63 #if $functions.bmerge.set == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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64 && mkdir bmerge_files
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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65 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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66 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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67 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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68 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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69 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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70
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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71
5
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
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72 #if $inputs.inputs.filetype == 'bfile':
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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73 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
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74 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
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75 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam
5
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
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76 && plink --bfile plink_input/plink_input
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
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77 #elif $inputs.inputs.filetype == 'vcf':
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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78 #if $inputs.inputs.input.is_of_type('bcf'):
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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79 && plink --bcf '$inputs.inputs.input'
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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80 #else:
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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81 && plink --vcf '$inputs.inputs.input'
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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82 #end if
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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83 #end if
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents: 4
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84
18be55ee8e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
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85 ## Plink commands by section
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
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86 #if $inputs.covar_input:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
87 --covar '$inputs.covar_input'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
88 #end if
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
89 #if $inputs.set_pheno.set_pheno == 'Yes':
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
90 --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno
0
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 #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
93 ##ID list functions
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
94 #if $functions.id_list.func == 'keep':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
95 --keep '$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
96 #elif $functions.id_list.func == 'keep-fam':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
97 --keep-fam '$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
98 #elif $functions.id_list.func == 'remove':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
99 --remove '$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
100 #elif $functions.id_list.func == 'remove-fam':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
101 --remove-fam '$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
102 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
103
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
104 ##Extraction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
105 #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
106 --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
107 #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
108 --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
109 #end if
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 ##Chromosome-specificity
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
112 #if $functions.chromosome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
113 --chr $functions.chromosome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
114 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
115
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
116 #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
117 --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
118 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
119
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
120 $functions.extra_chromosomes
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
121
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
122 #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
123 $functions.autosome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
124 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
125
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
126 ##SNP specificity
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
127 #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
128 --snps-only
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
129 #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
130 'just-acgt'
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 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
133
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
134 ##Variant windows
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
135 #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
136 #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
137 #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
138 --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
139 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
140 #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
141 --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
142 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
143 #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
144 #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
145 --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
146 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
147 #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
148 --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
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 #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
151 --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
152 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
153 #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
154 #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
155 --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
156 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
157 #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
158 --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
159 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
160 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
161 #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
162 $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
163 #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
164 --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
165 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
166 #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
167 --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
168 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
169 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
170
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
171 ##Thinning
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
172 #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
173 #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
174 --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
175 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
176 #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
177 --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
178 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
179 #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
180 --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
181 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
182 #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
183 --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
184 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
185 #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
186 --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
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 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
189
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
190 ##Pheno/covariate
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
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
193 ###########
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
194
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
195 ##Missing genotype rates
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
196 #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
197 --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
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.geno_rates.mind:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
200 --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
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
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
203 ##Allele Frequencies
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
204 #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
205 --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
206 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
207 #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
208 --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
209 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
210 #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
211 --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
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 #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
214 --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
215 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
216
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
217 ## Hardy-Weinberg
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
218 #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
219 --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
220 #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
221 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
222 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
223 #end if
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 ##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
226 #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
227 $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
228 #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
229 $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
230 #end if
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
231 $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
232 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
233
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
234 #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
235
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
236 #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
237 --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
238 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
239
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
240 #if $functions.template:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
241 --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
242 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
243
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
244 $functions.recode
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
245
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
246 #if $functions.flip:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
247 --flip $functions.flip
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
248 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
249
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
250 #if $functions.length:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
251 --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
252 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
253
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
254 #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
255 --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
256 #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
257 --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
258 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
259 #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
260 --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
261 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
262 #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
263 --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
264 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
265 #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
266 $functions.freq
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
267 $functions.hardy
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
268 $functions.missing
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
269 $functions.het
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
270 #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
271 $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
272 #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
273 $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
274 #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
275 $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
276 $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
277 $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
278 $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
279 #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
280 $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
281 $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
282 #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
283 $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
284 $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
285 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
286 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
287 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
288
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
289
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
290 #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
291 #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
292 --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
293 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
294 ## #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
295 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
296 ## #elif $functions.func == 'dist_sim':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
297 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
298 #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
299 #if $functions.read_genome:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
300 --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
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 #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
303 --cluster
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
304 #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
305 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
306 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
307 #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
308 --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
309 #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
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diff changeset
310 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
311 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
312 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
313 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
314
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
315 #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
316 #if $functions.assoc.assoc == 'Yes':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
317 --assoc
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
318 #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
319 perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
320 #elif $functions.assoc.perm.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
321 mperm='$functions.assoc.perm.value'
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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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 $functions.assoc.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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diff changeset
324 $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
325 $functions.assoc.fisher
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
326 $functions.assoc.count
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
327 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
328 #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
329 --adjust
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
330 #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
331 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
332 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
333 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
334 ## #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
335 ## --linear
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
336 ## #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
337 ## perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
338 ## #elif $functions.linear.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
339 ## mperm='$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
340 ## #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
341 ## $functions.linear.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
342 ## $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
343 ## $functions.linear.dominance
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
344 ## $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
345 ## $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
346 ## $functions.linear.interaction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
347 ## $functions.linear.beta
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
348 ## $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
349 ## $functions.linear.intercept
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
350 ## #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
351 #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
352 --logistic
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
353 #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
354 perm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
355 #elif $functions.logistic.perm.perm == 'mperm':
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
356 mperm='$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
357 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
358 $functions.logistic.genedrop
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
359 $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
360 $functions.logistic.dominance
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
361 $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
362 $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
363 $functions.logistic.interaction
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
364 $functions.logistic.beta
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
365 $functions.logistic.intercept
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
366 #end if
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
367 --lambda $functions.lambda
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
368 #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
369 #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
370 --genome
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
371 #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
372 $type
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
373 #end for
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
374 #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
375 --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
376 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
377 #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
378 --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
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 #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
381 --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
382 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
383 #end if
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
384
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
385 ## #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
386 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
387 ## #else:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
388 ## --rerun $functions.logfile
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
389 ##
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
390 #end if
6
f76d842e960f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 7faeca2291b3184038174dd44ca60e2fa33db179"
iuc
parents: 5
diff changeset
391 --memory \${GALAXY_MEMORY_MB:-8192}
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
392 --make-bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
393 --out plink_output/plink_output
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
394
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
395 #if $functions.func == 'association':
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
396 #if $functions.logistic.logistic == 'Yes':
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
397 && mkdir logistic_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
398 && mv plink_output/plink_output.*.l* logistic_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
399 && find ./logistic_out/. -type f -exec mv {} {}.txt ';'
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
400 #end if
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
401 #if $functions.adjust.adjust == 'Yes':
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
402 && mkdir adjust_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
403 && mv ./plink_output/*.adjuste* adjust_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
404 && find ./adjust_out/. -type f -exec mv {} {}.txt ';'
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
405 #end if
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
406 #if $functions.assoc.assoc == 'Yes':
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
407 && mkdir assoc_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
408 && mv ./plink_output/*asso* assoc_out
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
409 && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
410 #end if
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
411 #end if
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
412 && mkdir '$plink_out.extra_files_path'
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
413 && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
414 && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
415 && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
416 ]]></command>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
417 <inputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
418 <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
419 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
420 <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
421 <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
422 <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
423 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
424 <when value='bfile'>
2
0d43871f45ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 3ba5c41a39870355d1ba5dfc10a49e84d6135981"
iuc
parents: 1
diff changeset
425 <param format='pbed' name='bed' type='data' label='plink bed file'/>
0
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='vcf'>
4
ac16d24f0d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"
iuc
parents: 3
diff changeset
428 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
0
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 </conditional>
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
431 <conditional name='set_pheno'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
432 <param name='set_pheno' type='select' label='Set phenotype'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
433 <option value=''>No</option>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
434 <option value='Yes'>Yes</option>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
435 </param>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
436 <when value=''/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
437 <when value='Yes'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
438 <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.'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
439 <param name='all_pheno' type='boolean' truevalue='--all-pheno' falsevalue='' label='Allow all phenotypes present in the phenotype file to be subject to the association tests you have requested' checked='false'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
440 </when>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
441 </conditional>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
442 <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
443 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
444 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
445 <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
446 <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
447 <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
448 <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
449 <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
450 <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
451 <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
452 <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
453 <!-- <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
454 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
455 <when value='filtering'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
456 <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
457 <param name='func' type='select' label='ID list functions'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
458 <option value='none'>None</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
459 <option value='keep'>Keep by sample IDs</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
460 <option value='keep-fam'>Keep by family IDs</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
461 <option value='remove'>Remove by sample IDs</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
462 <option value='remove-fam'>Remove by family IDs</option>
0
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='keep'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
466 <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
467 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
468 <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
469 <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
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='remove'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
472 <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
473 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
474 <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
475 <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
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 <conditional name='extraction'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
479 <param name='ex_func' type='select' label='ID extraction functions'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
480 <option value='none'>None</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
481 <option value='extract'>Keep by variant IDs</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
482 <option value='exclude'>Remove by variant IDs </option>
0
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 <when value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
485 <when value='extract'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
486 <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
487 <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
488 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
489 <when value='exclude'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
490 <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
491 <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
492 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
493 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
494 <!-- <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
495 <!-- <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
496 <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
497 <option value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
498 <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
499 <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
500 <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
501 <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
502 <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
503 <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
504 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
505 <when value='none'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
506 <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
507 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
508 <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
509 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
510 <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
511 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
512 <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
513 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
514 <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
515 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
516 <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
517 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
518 </conditional> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
519 <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
520 <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
521 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
522 <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
523 <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
524 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
525 <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
526 <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
527 <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
528 <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
529 <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
530 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
531 <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
532 <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
533 <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
534 <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
535 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
536 <conditional name='ranges'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
537 <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
538 <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
539 <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
540 <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
541 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
542 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
543 <when value='single'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
544 <conditional name='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
545 <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
546 <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
547 <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
548 <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
549 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
550 <when value='variant'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
551 <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
552 <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
553 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
554 <when value='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
555 <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
556 <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
557 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
558 <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
559 <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
560 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
561 <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
562 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
563 <when value='range'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
564 <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
565 <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
566 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
567 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
568 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
569 <when value='multi'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
570 <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
571 (--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
572 --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
573 <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
574 <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
575 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
576 <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
577 <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
578 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
579 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
580 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
581 <conditional name='thinning'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
582 <param name='thinning' type='select' label='Arbitrary thinning'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
583 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
584 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
585 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
586 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
587 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
588 <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
589 <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
590 <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
591 <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
592 <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
593 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
594 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
595 <!-- <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
596 <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
597 <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
598 <option value='phenotype'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
599 <option value='Covariate'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
600 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
601 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
602 <when value='phenotype'> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
603 <!-- 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
604 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
605 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
606 keep-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
607 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
608 remove-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
609 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
610 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
611 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
612 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
613 <when value='Covariate'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
614 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
615 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
616 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
617 keep-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
618 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
619 remove-cats <filename>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
620 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
621 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
622 </conditional> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
623 <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
624 <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
625 <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
626 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
627 <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
628 <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
629 <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
630 <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
631 <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
632 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
633 <conditional name='hwe'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
634 <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
635 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
636 <option value='Yes'>Yes</option>
0
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 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
641 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
642 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
643 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
644 <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
645 <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
646 <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
647 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
648 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
649 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
650 <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
651 <param name='filter' type='select' label='Filter on sex and/or founders'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
652 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
653 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
654 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
655 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
656 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
657 <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
3
57ac42ec1be3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit fa78db02447a8f83bd61825eff2d58f449c0280b"
iuc
parents: 2
diff changeset
658 <option value=''>Do not specifically filter out based on sex or founders</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
659 <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
660 <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
661 <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
662 <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
663 <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
664 <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
665 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
666 <param name='no_sex_select' type='select' label='No sex settings' optional='true' help='How to deal with ambiguous sex phenotypes'>
3
57ac42ec1be3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit fa78db02447a8f83bd61825eff2d58f449c0280b"
iuc
parents: 2
diff changeset
667 <option value=''>Change nothing with regards to ambiguous sex samples</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
668 <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
669 <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
670 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
671 <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
672 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
673 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
674 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
675 <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
676 <conditional name='bmerge'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
677 <param name='set' type='select' label='Merge plink tilesets'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
678 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
679 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
680 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
681 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
682 <when value='Yes'>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
683 <param format='pbed' name='bed' type='data' label='plink bed file'/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
684 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
685 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
686 <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
687 <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
688 <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
689 <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
690 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
691 <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
692 <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
693 <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
694 <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
695 <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
696 <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
697 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
698 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
699 <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
700 <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
701 <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
702 <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
703 <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
704 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
705 <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
706 <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
707 <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
708 <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
709 <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
710 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
711 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
712 <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
713 <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
714 <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
715 <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
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='no'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
718 <when value='yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
719 <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
720 <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
721 <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
722 <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
723 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
724 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
725 <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
726 <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
727 <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
728 <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
729 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
730 <when value='no'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
731 <when value='yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
732 <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
733 <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
734 <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
735 <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
736 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
737 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
738 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
739 <when value='stats'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
740 <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
741 <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
742 <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
743 <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
744 <conditional name='sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
745 <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
746 <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
747 <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
748 <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
749 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
750 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
751 <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
752 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
753 <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
754 <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
755 <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
756 <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
757 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
758 <when value=''>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
759 <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
760 <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
761 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
762 <when value='ycount'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
763 <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
764 <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
765 <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
766 <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
767 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
768 <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
769 <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
770 <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
771 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
772 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
773 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
774 <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
775 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
776 <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
777 <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
778 <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
779 <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
780 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
781 <when value=''>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
782 <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
783 <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
784 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
785 <when value='ycount'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
786 <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
787 <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
788 <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
789 <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
790 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
791 <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
792 <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
793 <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
794 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
795 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
796 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
797 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
798 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
799 <when value='link'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
800 <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
801 <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
802 <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
803 <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
804 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
805 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
806 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
807 <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
808 <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
809 <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
810 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
811 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
812 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
813 <when value='stratification'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
814 <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
815 <conditional name='cluster'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
816 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
817 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
818 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
819 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
820 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
821 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
822 <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
823 <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
824 <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
825 <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
826 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
827 <conditional name='mds'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
828 <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
829 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
830 <option value='Yes'>Yes</option>
0
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 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
833 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
834 <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
835 <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
836 <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
837 <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
838 <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
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>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
841 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
842 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
843 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
844 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
845 <when value='association'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
846 <conditional name='assoc'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
847 <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
848 <option value=''>No</option>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
849 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
850 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
851 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
852 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
853 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
854 <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
855 <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
856 <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
857 <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
858 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
859 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
860 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
861 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
862 <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
863 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
864 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
865 <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
866 <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
867 <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
868 <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
869 <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
870 <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
871 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
872 <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
873 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
874 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
875 <conditional name='adjust'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
876 <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
877 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
878 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
879 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
880 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
881 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
882 <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
883 <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
884 <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
885 <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
886 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
887 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
888 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
889 <!-- <conditional name='linear'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
890 <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
891 <option value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
892 <option value='Yes'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
893 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
894 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
895 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
896 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
897 <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
898 <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
899 <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
900 <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
901 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
902 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
903 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
904 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
905 <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
906 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
907 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
908 <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
909 <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
910 <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
911 <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
912 <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
913 <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
914 <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
915 <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
916 <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
917 <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
918 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
919 <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
920 <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
921 <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
922 <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
923 <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
924 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
925 <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
926 <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
927 <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
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 <conditional name='logistic'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
932 <param name='logistic' type='select' label='Perform logistic regression and return report'>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
933 <option value='No'>No</option>
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
934 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
935 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
936 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
937 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
938 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
939 <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
940 <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
941 <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
942 <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
943 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
944 <when value='No'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
945 <when value='perm'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
946 <when value='mperm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
947 <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
948 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
949 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
950 <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
951 <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
952 <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
953 <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
954 <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
955 <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
956 <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
957 <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
958 <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
959 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
960 <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
961 <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
962 <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
963 <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
964 <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
965 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
966 <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
967 <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
968 <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
969 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
970 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
971 <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
972 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
973 <!-- <when value='scoring'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
974 </when> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
975 <when value='ibd'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
976 <conditional name='genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
977 <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
978 <option value=''>No</option>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
979 <option value='Yes'>Yes</option>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
980 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
981 <when value=''/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
982 <when value='Yes'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
983 <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
984 <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
985 <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
986 <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
987 <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
988 <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
989 <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
990 <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
991 </param>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
992 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
993 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
994 </when>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
995 <!-- <when value='rerun'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
996 <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
997 </when> -->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
998 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
999 </inputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1000 <outputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1001 <!--Main-->
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1002 <data name="plink_out" format="pbed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1003
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1004 <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1005
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1006 <!--Data Manage-->
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1007 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1008 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1009 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1010 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1011 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1012 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1013
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1014 <!--Stats-->
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1015 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1016 <filter>functions['func'] == 'stats' and functions['freq']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1017 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1018 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1019 <filter>functions['func'] == 'stats' and functions['hardy']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1020 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1021 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1022 <filter>functions['func'] == 'stats' and functions['missing']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1023 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1024 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1025 <filter>functions['func'] == 'stats' and functions['missing']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1026 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1027 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1028 <filter>functions['func'] == 'stats' and functions['het']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1029 </data>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1030 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1031 <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
1032 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1033
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1034 <!--Association-->
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1035 <!--Assoc -->
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1036 <collection name='assoc_outfiles' type='list' label='Association outfiles'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1037 <discover_datasets directory='assoc_out' pattern='__name_and_ext__'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1038 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes'</filter>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1039 </collection>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1040 <!--Adjust-->
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1041 <collection name='adjust_outfiles' type='list' label='Adjust outfiles'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1042 <discover_datasets directory='adjust_out' pattern='__name_and_ext__'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1043 <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes'</filter>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1044 </collection>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1045 <!--Logistic-->
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1046 <collection name='log_outfiles' type='list' label='Logistic outfiles'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1047 <discover_datasets directory='logistic_out' pattern='__name_and_ext__'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1048 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1049 </collection>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1050 <!--Link-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1051 <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
1052 <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
1053 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1054 <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1055 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1056 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1057
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1058 <!--IBD-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1059 <data name='genome' format='tabular' from_work_dir='plink_output/plink_output.genome' label='${tool.name}: Genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1060 <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
1061 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1062
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1063 <!--Stratifiction-->
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1064 <data name='mds' format='txt' from_work_dir='plink_output/plink_output.mds' label='${tool.name}: MDS'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1065 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1066 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1067 <data name='cluster1' format='tabular' from_work_dir='plink_output/plink_output.cluster1' label='${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
1068 <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
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='cluster2' format='tabular' from_work_dir='plink_output/plink_output.cluster2' label='${tool.name}: Cluster 2'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1071 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes'</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1072 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1073 <data name='cluster3' format='tabular' from_work_dir='plink_output/plink_output.cluster3' label='${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
1074 <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
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='cluster3missing' format='tabular' from_work_dir='plink_output/plink_output.cluster3.missing' label='${tool.name}: Cluster 3 missing'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1077 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['modifiers'] and 'missing' in functions['cluster']['modifiers']</filter>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1078 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1079 <data name='mds_miss' format='tabular' from_work_dir='plink_output/plink_output.mdist.missing' label='${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
1080 <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
1081 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1082 <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
1083 <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
1084 </data>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1085 </outputs>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1086 <tests>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1087 <test expect_num_outputs='2'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1088 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1089 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1090 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1091 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1092 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1093 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1094 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1095 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1096 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1097 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1098 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1099 <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
1100 <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
1101 <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
1102 <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
1103 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1104 <conditional name='extraction'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1105 <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
1106 <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
1107 <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
1108 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1109 <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
1110 <conditional name='ranges'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1111 <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
1112 <conditional name='window'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1113 <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
1114 <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
1115 <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
1116 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1117 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1118 <conditional name='thinning'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1119 <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
1120 <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
1121 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1122 <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
1123 <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
1124 <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
1125 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1126 <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
1127 <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
1128 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1129 <conditional name='hwe'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1130 <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
1131 <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
1132 <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
1133 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1134 <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
1135 <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
1136 <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
1137 <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
1138 <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
1139 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1140 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1141 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1142 <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1143 <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1144 <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1145 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1146 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1147 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1148
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1149 <test expect_num_outputs='4'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1150 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1151 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1152 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1153 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1154 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1155 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1156 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1157 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1158 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1159 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1160 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1161 <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
1162 <conditional name='bmerge'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1163 <param name='set' value='Yes'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1164 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1165 <composite_data value="plink_2.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1166 <composite_data value="plink_2.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1167 <composite_data value="plink_2.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1168 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1169 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1170 <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
1171 <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
1172 <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
1173 <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
1174 <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
1175 <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
1176 <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
1177 <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
1178 <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
1179 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1180 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1181 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1182 <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1183 <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1184 <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1185 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1186 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1187 <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
1188 <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
1189 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1190
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1191 <test expect_num_outputs='2'>
0
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='vcf'/>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1195 <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
1196 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1197 </section>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1198 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1199 <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1200 <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1201 <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1202 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1203 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1204 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1205
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1206 <test expect_num_outputs='8'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1207 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1208 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1209 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1210 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1211 <composite_data value="x_plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1212 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1213 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1214 </param>
0
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 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1217 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1218 <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
1219 <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
1220 <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
1221 <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
1222 <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
1223 <conditional name='sex'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1224 <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
1225 <conditional name='mode'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1226 <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
1227 <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
1228 <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
1229 <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
1230 <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
1231 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1232 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1233 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1234 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1235 <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1236 <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1237 <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1238 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1239 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1240 <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
1241 <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
1242 <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
1243 <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
1244 <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
1245 <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
1246 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1247
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1248 <test expect_num_outputs='4'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1249 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1250 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1251 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1252 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1253 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1254 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1255 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1256 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1257 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1258 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1259 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1260 <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
1261 <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
1262 <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
1263 <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
1264 <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
1265 <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
1266 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1267 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1268 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1269 <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1270 <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1271 <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1272 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1273 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1274 <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
1275 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1276
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1277 <test expect_num_outputs='7'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1278 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1279 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1280 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1281 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1282 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1283 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1284 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1285 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1286 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1287 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1288 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1289 <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
1290 <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
1291 <conditional name='cluster'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1292 <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
1293 <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
1294 <conditional name='mds'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1295 <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
1296 <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
1297 <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
1298 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1299 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1300 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1301 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1302 <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1303 <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1304 <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1305 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1306 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1307 <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
1308 <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
1309 <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
1310 <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
1311 <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
1312 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1313
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1314 <test expect_num_outputs='5'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1315 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1316 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1317 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1318 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1319 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1320 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1321 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1322 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1323 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1324 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1325 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1326 <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
1327 <conditional name='assoc'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1328 <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
1329 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1330 <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
1331 <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
1332 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1333 <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
1334 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1335 <conditional name='adjust'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1336 <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
1337 <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
1338 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1339 <conditional name='logistic'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1340 <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
1341 <conditional name='perm'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1342 <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
1343 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1344 <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
1345 <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
1346 <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
1347 <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
1348 <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
1349 <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
1350 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1351 <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
1352 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1353 <output name="plink_out">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1354 <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1355 <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1356 <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1357 </output>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1358 <expand macro="log_out_assert"/>
7
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1359 <output_collection name='assoc_outfiles' type='list' count='2'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1360 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1361 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1362 </output_collection>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1363 <output_collection name='adjust_outfiles' type='list' count='1'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1364 <element name='plink_output.assoc.fisher.adjusted' value='out.assoc.fisher.adjusted' compare='sim_size' />
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1365 </output_collection>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1366 <output_collection name='log_outfiles' type='list' count='3'>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1367 <element name='plink_output.assoc.logistic' value='out.assoc.logistic'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1368 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1369 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/>
66b35562554d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
iuc
parents: 6
diff changeset
1370 </output_collection>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1371 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1372
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1373 <test expect_num_outputs='3'>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1374 <section name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1375 <conditional name='inputs'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1376 <param name='filetype' value='bfile'/>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1377 <param name='bed' value='' ftype="pbed">
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1378 <composite_data value="plink.bim"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1379 <composite_data value="plink.bed"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1380 <composite_data value="plink.fam"/>
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1381 </param>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1382 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1383 </section>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1384 <conditional name='functions'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1385 <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
1386 <conditional name='genome'>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1387 <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
1388 <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
1389 <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
1390 <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
1391 </conditional>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1392 </conditional>
9
272aca44b3dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
iuc
parents: 8
diff changeset
1393 <expand macro="log_out_assert"/>
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1394 <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
1395 </test>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1396 </tests>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1397 <help><![CDATA[
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1398 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
1399
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1400 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
1401 ]]></help>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1402 <citations>
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1403 <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
1404 </citations>
8
16d22eee0fe3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
iuc
parents: 7
diff changeset
1405 </tool>