Mercurial > repos > iuc > plink
annotate plink.xml @ 6:f76d842e960f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 7faeca2291b3184038174dd44ca60e2fa33db179"
| author | iuc |
|---|---|
| date | Wed, 30 Sep 2020 20:29:06 +0000 |
| parents | 18be55ee8e08 |
| children | 66b35562554d |
| rev | line source |
|---|---|
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
2 <macros> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
3 <token name='@TOOL_VERSION@'>1.9.b618</token> |
|
6
f76d842e960f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 7faeca2291b3184038174dd44ca60e2fa33db179"
iuc
parents:
5
diff
changeset
|
4 <token name='@VERSION_SUFFIX@'>1</token> |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
5 <xml name='template_sanitizer'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
6 <sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
7 <valid initial='default'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
8 <add value='#' /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
9 <add value='@' /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
10 <add value='$'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
11 <add value='['/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
12 <add value=']'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
13 <add value='\'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
14 <remove value='"'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
15 <remove value='''/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
16 </valid> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
17 </sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
18 </xml> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
19 <xml name='chr_sanitizer'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
20 <sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
21 <valid initial='string.digits'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
22 <add value='X' /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
23 <add value='Y' /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
24 <add value=' ' /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
25 </valid> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
26 </sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
27 </xml> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
28 <xml name='snp_sanitizer'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
29 <sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
30 <valid initial='string.ascii_letters + string.digits'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
31 </sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
32 </xml> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
33 <xml name='snp_space_sanitizer'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
34 <sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
35 <valid initial='string.ascii_letters + string.digits'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
36 <add value=' '/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
37 </valid> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
38 </sanitizer> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
39 </xml> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
40 </macros> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
41 <requirements> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
42 <requirement type='package' version='1.90b6.18'>plink</requirement> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
43 </requirements> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
44 <command detect_errors='exit_code'><![CDATA[ |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
45 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
46 ## Create Plink folder for any inputs |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
47 mkdir ./plink_output |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
48 && mkdir ./plink_input |
|
5
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
49 |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
50 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
51 ## If bmerge is set, create folder for merged files |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
52 #if $functions.func == 'data_manage': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
53 #if $functions.bmerge.set == 'Yes': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
54 && mkdir bmerge_files |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
55 && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
56 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
57 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
58 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
59 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
60 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
61 |
|
5
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
62 #if $inputs.inputs.filetype == 'bfile': |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
63 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
64 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
65 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
66 && plink --bfile plink_input/plink_input |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
67 #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
diff
changeset
|
68 #if $inputs.inputs.input.is_of_type('bcf'): |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
69 && plink --bcf '$inputs.inputs.input' |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
70 #else: |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
71 && 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
diff
changeset
|
72 #end if |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
73 #end if |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
74 |
|
18be55ee8e08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
iuc
parents:
4
diff
changeset
|
75 ## Plink commands by section |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
76 #if $inputs.covar_input: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
77 --covar '$inputs.covar_input' |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
78 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
79 #if $inputs.pheno: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
80 --pheno $inputs.pheno |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
81 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
82 #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
|
83 ##ID list functions |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
84 #if $functions.id_list.func == 'keep': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
85 --keep '$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
|
86 #elif $functions.id_list.func == 'keep-fam': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
87 --keep-fam '$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
|
88 #elif $functions.id_list.func == 'remove': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
89 --remove '$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
|
90 #elif $functions.id_list.func == 'remove-fam': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
91 --remove-fam '$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
|
92 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
93 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
94 ##Extraction |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
95 #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
|
96 --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
|
97 #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
|
98 --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
|
99 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
100 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
101 ##Chromosome-specificity |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
102 #if $functions.chromosome: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
103 --chr $functions.chromosome |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
104 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
105 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
106 #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
|
107 --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
|
108 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
109 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
110 $functions.extra_chromosomes |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
111 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
112 #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
|
113 $functions.autosome |
|
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 ##SNP specificity |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
117 #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
|
118 --snps-only |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
119 #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
|
120 'just-acgt' |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
121 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
122 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
123 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
124 ##Variant windows |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
125 #if $functions.ranges.single_multi == 'single': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
126 #if $functions.ranges.window.type == 'variant': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
127 #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
|
128 --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
|
129 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
130 #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
|
131 --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
|
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 #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
|
134 #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
|
135 --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
|
136 #end if |
|
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.exclude_snp: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
138 --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
|
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.window: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
141 --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
|
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 #else: |
|
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.from_bp: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
145 --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
|
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.to_bp: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
148 --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
|
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 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
151 #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
|
152 $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
|
153 #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
|
154 --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
|
155 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
156 #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
|
157 --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
|
158 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
159 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
160 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
161 ##Thinning |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
162 #if $functions.thinning.thinning == 'Yes': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
163 #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
|
164 --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
|
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.thinning.thin_count: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
167 --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
|
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 #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
|
170 --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
|
171 #end if |
|
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.thin_indiv: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
173 --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
|
174 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
175 #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
|
176 --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
|
177 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
178 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
179 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
180 ##Pheno/covariate |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
181 ########### |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
182 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
183 ########### |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
184 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
185 ##Missing genotype rates |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
186 #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
|
187 --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
|
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 #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
|
190 --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
|
191 #end if |
|
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 ##Allele Frequencies |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
194 #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
|
195 --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
|
196 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
197 #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
|
198 --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
|
199 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
200 #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
|
201 --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
|
202 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
203 #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
|
204 --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
|
205 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
206 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
207 ## Hardy-Weinberg |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
208 #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
|
209 --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
|
210 #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
|
211 $type |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
212 #end for |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
213 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
214 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
215 ##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
|
216 #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
|
217 $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
|
218 #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
|
219 $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
|
220 #end if |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
221 $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
|
222 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
223 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
224 #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
|
225 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
226 #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
|
227 --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
|
228 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
229 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
230 #if $functions.template: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
231 --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
|
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 $functions.recode |
|
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.flip: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
237 --flip $functions.flip |
|
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.length: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
241 --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
|
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 #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
|
245 --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
|
246 #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
|
247 --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
|
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 #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
|
250 --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
|
251 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
252 #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
|
253 --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
|
254 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
255 #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
|
256 $functions.freq |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
257 $functions.hardy |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
258 $functions.missing |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
259 $functions.het |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
260 #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
|
261 $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
|
262 #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
|
263 $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
|
264 #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
|
265 $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
|
266 $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
|
267 $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
|
268 $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
|
269 #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
|
270 $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
|
271 $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
|
272 #else: |
|
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.female_max |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
274 $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
|
275 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
276 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
277 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
278 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
279 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
280 #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
|
281 #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
|
282 --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
|
283 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
284 ## #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
|
285 ## |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
286 ## #elif $functions.func == 'dist_sim': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
287 ## |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
288 #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
|
289 #if $functions.read_genome: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
290 --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
|
291 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
292 #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
|
293 --cluster |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
294 #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
|
295 $type |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
296 #end for |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
297 #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
|
298 --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
|
299 #for $type in $functions.cluster.mds.modifiers |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
300 $type |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
301 #end for |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
302 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
303 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
304 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
305 #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
|
306 #if $functions.assoc.assoc == 'Yes': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
307 --assoc |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
308 #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
|
309 perm |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
310 #elif $functions.assoc.perm.perm == 'mperm': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
311 mperm='$functions.assoc.perm.value' |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
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 $functions.assoc.genedrop |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
314 $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
|
315 $functions.assoc.fisher |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
316 $functions.assoc.count |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
317 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
318 #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
|
319 --adjust |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
320 #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
|
321 $type |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
322 #end for |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
323 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
324 ## #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
|
325 ## --linear |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
326 ## #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
|
327 ## perm |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
328 ## #elif $functions.linear.perm == 'mperm': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
329 ## mperm='$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
|
330 ## #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
331 ## $functions.linear.genedrop |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
332 ## $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
|
333 ## $functions.linear.dominance |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
334 ## $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
|
335 ## $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
|
336 ## $functions.linear.interaction |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
337 ## $functions.linear.beta |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
338 ## $functions.linear.standard_beta |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
339 ## $functions.linear.intercept |
|
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 #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
|
342 --logistic |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
343 #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
|
344 perm |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
345 #elif $functions.logistic.perm.perm == 'mperm': |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
346 mperm='$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
|
347 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
348 $functions.logistic.genedrop |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
349 $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
|
350 $functions.logistic.dominance |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
351 $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
|
352 $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
|
353 $functions.logistic.interaction |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
354 $functions.logistic.beta |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
355 $functions.logistic.intercept |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
356 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
357 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
358 #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
|
359 #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
|
360 --genome |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
361 #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
|
362 $type |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
363 #end for |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
364 #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
|
365 --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
|
366 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
367 #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
|
368 --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
|
369 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
370 #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
|
371 --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
|
372 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
373 #end if |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
374 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
375 ## #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
|
376 ## |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
377 ## #else: |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
378 ## --rerun $functions.logfile |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
379 ## |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
380 #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
|
381 --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
|
382 --make-bed |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
383 --out plink_output/plink_output |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
384 ]]></command> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
385 <inputs> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
386 <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
|
387 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
388 <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
|
389 <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
|
390 <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
|
391 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
392 <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
|
393 <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
|
394 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
395 <param format='txt' name='fam' type='data' label='plink fam file'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
396 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
397 <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
|
398 <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
|
399 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
400 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
401 <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
402 <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
|
403 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
404 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
405 <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
|
406 <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
|
407 <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
|
408 <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
|
409 <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
|
410 <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
|
411 <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
|
412 <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
|
413 <!-- <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
|
414 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
415 <when value='filtering'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
416 <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
|
417 <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
|
418 <option value='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
419 <option value='keep'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
420 <option value='keep-fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
421 <option value='remove'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
422 <option value='remove-fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
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='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
425 <when value='keep'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
426 <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
|
427 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
428 <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
|
429 <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
|
430 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
431 <when value='remove'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
432 <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
|
433 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
434 <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
|
435 <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
|
436 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
437 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
438 <conditional name='extraction'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
439 <param name='ex_func' type='select' label='ID extraction functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
440 <option value='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
441 <option value='extract'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
442 <option value='exclude'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
443 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
444 <when value='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
445 <when value='extract'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
446 <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
|
447 <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
|
448 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
449 <when value='exclude'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
450 <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
|
451 <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
|
452 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
453 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
454 <!-- <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
|
455 <!-- <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
|
456 <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
|
457 <option value='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
458 <option value='extract-col-cond'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
459 <option value='extract-col-cond-match'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
460 <option value='extract-col-cond-mismatch'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
461 <option value='extract-col-cond-substr'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
462 <option value='extract-col-cond-min'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
463 <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
|
464 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
465 <when value='none'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
466 <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
|
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='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
|
469 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
470 <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
|
471 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
472 <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
|
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='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
|
475 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
476 <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
|
477 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
478 </conditional> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
479 <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
|
480 <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
|
481 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
482 <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
|
483 <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
|
484 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
485 <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
|
486 <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
|
487 <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
|
488 <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
|
489 <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
|
490 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
491 <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
|
492 <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
|
493 <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
|
494 <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
|
495 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
496 <conditional name='ranges'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
497 <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
|
498 <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
|
499 <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
|
500 <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
|
501 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
502 <when value=''/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
503 <when value='single'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
504 <conditional name='window'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
505 <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
|
506 <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
|
507 <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
|
508 <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
|
509 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
510 <when value='variant'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
511 <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
|
512 <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
|
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='window'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
515 <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
|
516 <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
|
517 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
518 <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
|
519 <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
|
520 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
521 <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
|
522 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
523 <when value='range'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
524 <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
|
525 <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
|
526 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
527 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
528 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
529 <when value='multi'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
530 <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
|
531 (--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
|
532 --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
|
533 <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
|
534 <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
|
535 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
536 <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
|
537 <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
|
538 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
539 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
540 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
541 <conditional name='thinning'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
542 <param name='thinning' type='select' label='Arbitrary thinning'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
543 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
544 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
545 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
546 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
547 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
548 <param name='thin' 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
|
549 <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
|
550 <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
|
551 <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
|
552 <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
|
553 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
554 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
555 <!-- <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
|
556 <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
|
557 <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
|
558 <option value='phenotype'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
559 <option value='Covariate'/> |
|
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 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
562 <when value='phenotype'> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
563 <!-- 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
|
564 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
|
565 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
|
566 keep-cats <filename> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
567 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
|
568 remove-cats <filename> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
569 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
|
570 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
|
571 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
|
572 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
573 <when value='Covariate'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
574 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
|
575 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
|
576 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
|
577 keep-cats <filename> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
578 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
|
579 remove-cats <filename> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
580 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
|
581 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
582 </conditional> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
583 <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
|
584 <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
|
585 <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
|
586 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
587 <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
|
588 <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
|
589 <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
|
590 <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
|
591 <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
|
592 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
593 <conditional name='hwe'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
594 <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
595 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
596 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
597 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
598 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
599 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
600 <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
|
601 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
|
602 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
|
603 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
|
604 <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
|
605 <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
|
606 <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
|
607 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
608 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
609 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
610 <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
|
611 <param name='filter' type='select' label='Filter on sex and/or founders'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
612 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
613 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
614 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
615 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
616 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
617 <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
|
618 <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
|
619 <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
|
620 <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
|
621 <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
|
622 <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
|
623 <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
|
624 <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
|
625 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
626 <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
|
627 <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
|
628 <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
|
629 <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
|
630 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
631 <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
|
632 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
633 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
634 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
635 <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
|
636 <conditional name='bmerge'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
637 <param name='set' type='select' label='Merge plink tilesets'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
638 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
639 <option 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> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
641 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
642 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
643 <param format='binary' name='bed' type='data' label='plink bed file'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
644 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
645 <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
646 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
647 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
648 <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
|
649 <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
|
650 <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
|
651 <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
|
652 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
653 <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
|
654 <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
|
655 <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
|
656 <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
|
657 <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
|
658 <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
|
659 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
660 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
661 <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
|
662 <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
|
663 <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
|
664 <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
|
665 <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
|
666 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
667 <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
|
668 <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
|
669 <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
|
670 <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
|
671 <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
|
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 <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
|
675 <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
|
676 <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
|
677 <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
|
678 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
679 <when value='no'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
680 <when value='yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
681 <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
|
682 <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
|
683 <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
|
684 <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
|
685 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
686 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
687 <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
|
688 <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
|
689 <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
|
690 <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
|
691 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
692 <when value='no'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
693 <when value='yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
694 <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
|
695 <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
|
696 <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
|
697 <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
|
698 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
699 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
700 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
701 <when value='stats'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
702 <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
|
703 <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
|
704 <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
|
705 <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
|
706 <conditional name='sex'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
707 <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
|
708 <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
|
709 <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
|
710 <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
|
711 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
712 <when value=''/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
713 <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
|
714 <conditional name='mode'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
715 <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
|
716 <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
|
717 <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
|
718 <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
|
719 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
720 <when value=''> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
721 <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
|
722 <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
|
723 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
724 <when value='ycount'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
725 <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
|
726 <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
|
727 <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
|
728 <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
|
729 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
730 <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
|
731 <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
|
732 <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
|
733 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
734 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
735 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
736 <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
|
737 <conditional name='mode'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
738 <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
|
739 <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
|
740 <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
|
741 <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
|
742 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
743 <when value=''> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
744 <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
|
745 <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
|
746 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
747 <when value='ycount'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
748 <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
|
749 <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
|
750 <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
|
751 <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
|
752 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
753 <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
|
754 <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
|
755 <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
|
756 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
757 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
758 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
759 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
760 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
761 <when value='link'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
762 <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
|
763 <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
|
764 <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
|
765 <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
|
766 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
767 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
768 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
769 <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
|
770 <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
|
771 <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
|
772 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
773 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
774 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
775 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
776 <when value='stratification'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
777 <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
|
778 <conditional name='cluster'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
779 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
780 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
781 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
782 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
783 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
784 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
785 <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
|
786 <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
|
787 <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
|
788 <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
|
789 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
790 <conditional name='mds'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
791 <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
792 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
793 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
794 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
795 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
796 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
797 <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
|
798 <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
|
799 <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
|
800 <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
|
801 <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
|
802 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
803 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
804 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
805 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
806 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
807 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
808 <when value='association'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
809 <conditional name='assoc'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
810 <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
|
811 <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
|
812 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
813 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
814 <when value=''/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
815 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
816 <conditional name='perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
817 <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
|
818 <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
|
819 <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
|
820 <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
|
821 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
822 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
823 <when value='perm'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
824 <when value='mperm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
825 <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
|
826 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
827 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
828 <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
|
829 <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
|
830 <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
|
831 <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
|
832 <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
|
833 <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
|
834 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
835 <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
|
836 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
837 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
838 <conditional name='adjust'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
839 <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
840 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
841 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
842 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
843 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
844 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
845 <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
|
846 <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
|
847 <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
|
848 <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
|
849 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
850 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
851 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
852 <!-- <conditional name='linear'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
853 <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
|
854 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
855 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
856 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
857 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
858 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
859 <conditional name='perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
860 <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
|
861 <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
|
862 <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
|
863 <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
|
864 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
865 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
866 <when value='perm'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
867 <when value='mperm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
868 <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
|
869 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
870 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
871 <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
|
872 <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
|
873 <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
|
874 <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
|
875 <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
|
876 <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
|
877 <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
|
878 <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
|
879 <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
|
880 <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
|
881 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
882 <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
|
883 <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
|
884 <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
|
885 <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
|
886 <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
|
887 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
888 <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
|
889 <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
|
890 <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
|
891 <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
|
892 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
893 </conditional> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
894 <conditional name='logistic'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
895 <param name='logistic' type='select' label='Perform logistic regression and return report'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
896 <option value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
897 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
898 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
899 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
900 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
901 <conditional name='perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
902 <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
|
903 <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
|
904 <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
|
905 <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
|
906 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
907 <when value='No'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
908 <when value='perm'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
909 <when value='mperm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
910 <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
|
911 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
912 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
913 <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
|
914 <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
|
915 <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
|
916 <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
|
917 <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
|
918 <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
|
919 <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
|
920 <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
|
921 <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
|
922 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
923 <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
|
924 <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
|
925 <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
|
926 <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
|
927 <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
|
928 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
929 <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
|
930 <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
|
931 <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
|
932 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
933 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
934 <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
|
935 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
936 <!-- <when value='scoring'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
937 </when> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
938 <when value='ibd'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
939 <conditional name='genome'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
940 <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
|
941 <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
|
942 <option value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
943 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
944 <when value=''/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
945 <when value='Yes'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
946 <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
|
947 <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
|
948 <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
|
949 <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
|
950 <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
|
951 <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
|
952 <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
|
953 <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
|
954 </param> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
955 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
956 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
957 </when> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
958 <!-- <when value='rerun'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
959 <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
|
960 </when> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
961 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
962 </inputs> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
963 <outputs> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
964 <!--Main--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
965 <collection name='plink_out' type='list' label='Plink main outputs'> |
|
2
0d43871f45ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 3ba5c41a39870355d1ba5dfc10a49e84d6135981"
iuc
parents:
1
diff
changeset
|
966 <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/> |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
967 <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/> |
|
2
0d43871f45ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 3ba5c41a39870355d1ba5dfc10a49e84d6135981"
iuc
parents:
1
diff
changeset
|
968 <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/> |
|
0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
969 <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
970 </collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
971 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
972 <!--Data Manage--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
973 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
974 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
975 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
976 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
977 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
978 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
979 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
980 <!--Stats--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
981 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
982 <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
|
983 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
984 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
985 <filter>functions['func'] == 'stats' and functions['hardy']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
986 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
987 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
988 <filter>functions['func'] == 'stats' and functions['missing']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
989 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
990 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
991 <filter>functions['func'] == 'stats' and functions['missing']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
992 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
993 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
994 <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
|
995 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
996 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
997 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
998 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
999 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1000 <!--Association--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1001 <!--assoc--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1002 <data name='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1003 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1004 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1005 <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1006 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1007 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1008 <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association Max(T) permutation test'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1009 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and not functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1010 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1011 <data name='fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher' label='${tool.name}: Association Fisher'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1012 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1013 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1014 <data name='fisher_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.perm' label='${tool.name}: Association Fisher perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1015 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1016 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1017 <data name='fisher_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.mperm' label='${tool.name}: Association Fisher mperm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1018 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1019 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1020 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1021 <!--adjust--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1022 <data name='adjust' format='tabular' from_work_dir='plink_output/plink_output.assoc.adjusted' label='${tool.name}: Adjusted'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1023 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and not functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1024 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1025 <data name='adjust_fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.adjusted' label='${tool.name}: Fisher Adjusted'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1026 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and functions['assoc']['fisher']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1027 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1028 <data name='adjust_logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.adjusted' label='${tool.name}: Logistic Adjusted'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1029 <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes' and functions['logistic']['logistic'] == 'Yes'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1030 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1031 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1032 <!-- <data name='linear' format='tabular' from_work_dir='plink_output/plink_output.assoc.linenar' label='${tool.name}: Linear Regression'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1033 <filter>functions['func'] == 'association' and functions.func.association.linear['linear'] == 'Yes'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1034 </data> --> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1035 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1036 <!--Logistic--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1037 <data name='logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic' label='${tool.name}: Logistic Regression'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1038 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1039 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1040 <data name='logistic_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.perm' label='${tool.name}: Logistic Association Monte Carlo'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1041 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'perm'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1042 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1043 <data name='logistic_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.mperm' label='${tool.name}: Logistic Association Max(T) permutation test'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1044 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'mperm'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1045 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1046 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1047 <!--Link--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1048 <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1049 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1050 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1051 <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${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
|
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 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1055 <!--IBD--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1056 <data name='genome' format='tabular' from_work_dir='plink_output/plink_output.genome' label='${tool.name}: Genome'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1057 <filter>functions['func'] == 'ibd' and functions['genome']['output_genome']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1058 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1059 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1060 <!--Stratifiction--> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1061 <data name='mds' format='txt' from_work_dir='plink_output/plink_output.mds' label='${tool.name}: MDS'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1062 <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
|
1063 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1064 <data name='cluster1' format='tabular' from_work_dir='plink_output/plink_output.cluster1' label='${tool.name}: Cluster 1'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1065 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes'</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1066 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1067 <data name='cluster2' format='tabular' from_work_dir='plink_output/plink_output.cluster2' label='${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
|
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='cluster3' format='tabular' from_work_dir='plink_output/plink_output.cluster3' label='${tool.name}: Cluster 3'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1071 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and 'missing' not in functions['cluster']['modifiers']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1072 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1073 <data name='cluster3missing' format='tabular' from_work_dir='plink_output/plink_output.cluster3.missing' label='${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
|
1074 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['modifiers'] and 'missing' in functions['cluster']['modifiers']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1075 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1076 <data name='mds_miss' format='tabular' from_work_dir='plink_output/plink_output.mdist.missing' label='${tool.name}: Mdist missing'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1077 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['modifiers'] and 'missing' in functions['cluster']['modifiers']</filter> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1078 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1079 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1080 <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
|
1081 </data> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1082 </outputs> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1083 <tests> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1084 <test expect_num_outputs='5'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1085 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1086 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1087 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1088 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1089 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1090 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1091 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1092 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1093 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1094 <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
|
1095 <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
|
1096 <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
|
1097 <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
|
1098 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1099 <conditional name='extraction'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1100 <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
|
1101 <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
|
1102 <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
|
1103 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1104 <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
|
1105 <conditional name='ranges'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1106 <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
|
1107 <conditional name='window'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1108 <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
|
1109 <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
|
1110 <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
|
1111 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1112 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1113 <conditional name='thinning'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1114 <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
|
1115 <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
|
1116 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1117 <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
|
1118 <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
|
1119 <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
|
1120 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1121 <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
|
1122 <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
|
1123 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1124 <conditional name='hwe'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1125 <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
|
1126 <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
|
1127 <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
|
1128 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1129 <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
|
1130 <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
|
1131 <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
|
1132 <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
|
1133 <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
|
1134 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1135 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1136 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1137 <element name='plink_bed' file='test1_out.bed' compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1138 <element name='plink_bim' file='test1_out.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1139 <element name='plink_fam' file='test1_out.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1140 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1141 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1142 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1143 <test expect_num_outputs='7'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1144 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1145 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1146 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1147 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1148 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1149 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1150 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1151 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1152 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1153 <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
|
1154 <conditional name='bmerge'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1155 <param name='set' value='Yes'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1156 <param name='bed' value='plink_2.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1157 <param name='bim' value='plink_2.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1158 <param name='fam' value='plink_2.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1159 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1160 <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
|
1161 <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
|
1162 <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
|
1163 <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
|
1164 <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
|
1165 <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
|
1166 <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
|
1167 <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
|
1168 <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
|
1169 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1170 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1171 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1172 <element name='plink_bed' file='test2_out.bed' compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1173 <element name='plink_bim' file='test2_out.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1174 <element name='plink_fam' file='test2_out.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1175 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1176 <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
|
1177 <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
|
1178 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1179 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1180 <test expect_num_outputs='5'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1181 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1182 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1183 <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
|
1184 <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
|
1185 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1186 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1187 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1188 <element name='plink_bed' file='vcf_out.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1189 <element name='plink_bim' file='vcf_out.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1190 <element name='plink_fam' file='vcf_out.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1191 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1192 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1193 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1194 <test expect_num_outputs='11'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1195 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1196 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1197 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1198 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1199 <param name='bim' value='x_plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1200 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1201 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1202 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1203 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1204 <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
|
1205 <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
|
1206 <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
|
1207 <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
|
1208 <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
|
1209 <conditional name='sex'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1210 <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
|
1211 <conditional name='mode'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1212 <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
|
1213 <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
|
1214 <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
|
1215 <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
|
1216 <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
|
1217 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1218 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1219 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1220 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1221 <element name='plink_bed' file='stats.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1222 <element name='plink_bim' file='stats.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1223 <element name='plink_fam' file='stats.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1224 <element name='plink_fam' file='stats.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1225 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1226 <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
|
1227 <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
|
1228 <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
|
1229 <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
|
1230 <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
|
1231 <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
|
1232 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1233 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1234 <test expect_num_outputs='7'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1235 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1236 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1237 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1238 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1239 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1240 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1241 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1242 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1243 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1244 <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
|
1245 <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
|
1246 <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
|
1247 <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
|
1248 <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
|
1249 <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
|
1250 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1251 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1252 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1253 <element name='plink_bed' file='test5_out.bed' compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1254 <element name='plink_bim' file='test5_out.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1255 <element name='plink_fam' file='test5_out.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1256 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1257 <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
|
1258 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1259 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1260 <test expect_num_outputs='10'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1261 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1262 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1263 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1264 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1265 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1266 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1267 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1268 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1269 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1270 <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
|
1271 <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
|
1272 <conditional name='cluster'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1273 <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
|
1274 <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
|
1275 <conditional name='mds'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1276 <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
|
1277 <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
|
1278 <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
|
1279 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1280 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1281 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1282 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1283 <element name='plink_bed' file='test6_out.bed' compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1284 <element name='plink_bim' file='test6_out.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1285 <element name='plink_fam' file='test6_out.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1286 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1287 <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
|
1288 <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
|
1289 <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
|
1290 <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
|
1291 <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
|
1292 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1293 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1294 <test expect_num_outputs='11'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1295 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1296 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1297 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1298 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1299 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1300 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1301 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1302 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1303 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1304 <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
|
1305 <conditional name='assoc'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1306 <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
|
1307 <conditional name='perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1308 <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
|
1309 <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
|
1310 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1311 <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
|
1312 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1313 <conditional name='adjust'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1314 <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
|
1315 <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
|
1316 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1317 <conditional name='logistic'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1318 <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
|
1319 <conditional name='perm'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1320 <param name='perm' value='perm'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1321 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1322 <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
|
1323 <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
|
1324 <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
|
1325 <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
|
1326 <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
|
1327 <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
|
1328 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1329 <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
|
1330 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1331 <output_collection name='plink_out' type='list'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1332 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1333 <element name='plink_bim' file='out.assoc.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1334 <element name='plink_fam' file='out.assoc.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1335 </output_collection> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1336 <output name='fisher' value="out.assoc.fisher"/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1337 <output name='adjust_fisher' value="out.assoc.fisher.adjusted" sort="True" /> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1338 <output name='fisher_mperm' value="out.assoc.fisher.mperm" compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1339 <output name='logistic' value="out.assoc.logistic"/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1340 <output name='adjust_logistic' value="out.assoc.logistic.adjusted"/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1341 <output name='logistic_perm' value="out.assoc.logistic.perm" compare='sim_size'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1342 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1343 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1344 <test expect_num_outputs='6'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1345 <section name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1346 <conditional name='inputs'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1347 <param name='filetype' value='bfile'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1348 <param name='bed' value='plink.bed'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1349 <param name='bim' value='plink.bim'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1350 <param name='fam' value='plink.fam'/> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1351 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1352 </section> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1353 <conditional name='functions'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1354 <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
|
1355 <conditional name='genome'> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1356 <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
|
1357 <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
|
1358 <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
|
1359 <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
|
1360 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1361 </conditional> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1362 <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
|
1363 </test> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1364 </tests> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1365 <help><![CDATA[ |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1366 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
|
1367 |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1368 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
|
1369 ]]></help> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1370 <citations> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1371 <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
|
1372 </citations> |
|
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
|
1373 </tool> |