Mercurial > repos > iuc > gemini_burden
comparison gemini_burden.xml @ 4:c70d79e0eed7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author | iuc |
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date | Fri, 14 Dec 2018 13:03:59 -0500 |
parents | e799c1a6854b |
children | 699ce2631e79 |
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3:1a4c5adcd587 | 4:c70d79e0eed7 |
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> |
2 <description>perform sample-wise gene-level burden calculations</description> | 2 <description>perform sample-wise gene-level burden calculations</description> |
3 <macros> | 3 <macros> |
4 <import>gemini_macros.xml</import> | 4 <import>gemini_macros.xml</import> |
5 <token name="@BINARY@">burden</token> | 5 <token name="@BINARY@">burden</token> |
6 <token name="@GEMINI_BUG_WARNING@">Caveat: due to a bug in this version of GEMINI, filtering on alternate allele frequency will get disabled when you select 'All non-synonymous variants' as the types of variants to be used for the burden calculations above.</token> | |
6 </macros> | 7 </macros> |
7 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
8 <expand macro="stdio" /> | 9 <expand macro="stdio" /> |
9 <expand macro="version_command" /> | 10 <expand macro="version_command" /> |
10 <command> | 11 <command> |
11 <![CDATA[ | 12 <![CDATA[ |
12 gemini @BINARY@ | 13 gemini @BINARY@ |
13 --cases $cases | |
14 --controls $controls | |
15 $save_tscores | |
16 $nonsynonymous | 14 $nonsynonymous |
17 $calpha | 15 #if str($analysis.mode) == "c-alpha": |
18 --permutations $permutations | 16 --calpha |
19 #if float( str($min_aaf) ) >= 0.0: | 17 #if str($analysis.casecontrol.source) == "custom": |
20 --min-aaf $min_aaf | 18 --cases |
19 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.cases.strip().split()))# | |
20 --controls | |
21 #echo (" ".join("'" + token + "'" for token in $analysis.casecontrol.controls.strip().split()))# | |
22 #end if | |
23 --min-aaf ${analysis.min_aaf} | |
24 --max-aaf ${analysis.max_aaf} | |
25 --permutations ${analysis.permutations} | |
26 ${analysis.save_tscores} | |
21 #end if | 27 #end if |
22 #if float( str($max_aaf) ) >= 0.0: | 28 "$infile" |
23 --max-aaf $max_aaf | 29 > "$outfile" |
24 #end if | 30 #if str($analysis.mode) == "c-alpha" and $analysis.save_tscores: |
25 "${ infile }" | 31 && touch permutated_t_scores.txt |
26 > "${ outfile }" | 32 && mv permutated_t_scores.txt $t_scores |
33 #end if | |
27 ]]> | 34 ]]> |
28 | 35 |
29 </command> | 36 </command> |
30 <inputs> | 37 <inputs> |
31 <expand macro="infile" /> | 38 <expand macro="infile" /> |
32 | 39 <param argument="--non-synonymous" name="nonsynonymous" type="select" |
33 <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/> | 40 label="Use the following types of variants for the burden calculation"> |
34 <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/> | 41 <option value="">High impact variants only</option> |
35 | 42 <option value="--nonsynonymous">All non-synonymous variants</option> |
36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" | |
37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/> | |
38 | |
39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" | |
40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/> | |
41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" | |
42 label="Run the C-alpha association test" help="(--calpha)"/> | |
43 <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included" | |
44 help="(--min-aaf)"> | |
45 <!--validator type="in_range" min="0.0"/--> | |
46 </param> | 43 </param> |
47 <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included" | 44 <conditional name="analysis"> |
48 help="(--max-aaf)"> | 45 <param argument="--calpha" name="mode" type="select" |
49 <!--validator type="in_range" min="0.0"/--> | 46 label="Which type of burden calculation should be performed?"> |
50 </param> | 47 <option value="counts">Count of variants per gene and sample</option> |
51 | 48 <option value="c-alpha">C-alpha association test per gene</option> |
52 <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test" | 49 </param> |
53 help="(--permutations)"> | 50 <when value="counts" /> |
54 <validator type="in_range" min="0"/> | 51 <when value="c-alpha"> |
55 </param> | 52 <conditional name="casecontrol"> |
56 | 53 <param name="source" type="select" |
54 label="Selection of case and control samples" | |
55 help="Specify how case and control samples for the C-alpha association test should be selected"> | |
56 <option value="ped">Use PED file information</option> | |
57 <option value="custom">Custom selection</option> | |
58 </param> | |
59 <when value="ped" /> | |
60 <when value="custom"> | |
61 <param argument="--cases" name="cases" type="text" value="" | |
62 label="Space separated list of cases for association testing"/> | |
63 <param argument="--controls" name="controls" type="text" value="" | |
64 label="Space separated list of controls for association testing" help="(--controls)"/> | |
65 </when> | |
66 </conditional> | |
67 <param argument="--min-aaf" name="min_aaf" type="float" min="0" max="1" value="0" | |
68 label="The min. alt. allele frequency for a variant to be included" | |
69 help="@GEMINI_BUG_WARNING@" /> | |
70 <param argument="--max-aaf" name="max_aaf" type="float" min="0" max="1" value="1" | |
71 label="The max. alt. allele frequency for a variant to be included" | |
72 help="@GEMINI_BUG_WARNING@" /> | |
73 <param argument="--permutations" name="permutations" type="integer" min="1" value="100" label="Number of permutations to run for the C-alpha test" /> | |
74 <param argument="--save_tscores" name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" | |
75 label="Save the list of individual T-scores from all permutations as an extra dataset" /> | |
76 </when> | |
77 </conditional> | |
57 </inputs> | 78 </inputs> |
58 <outputs> | 79 <outputs> |
59 <data name="outfile" format="tabular" /> | 80 <data name="outfile" format="tabular" |
81 label="GEMINI burden ${analysis.mode} on ${on_string}" /> | |
82 <data name="t_scores" format="tabular" | |
83 label="GEMINI burden permuted T scores on ${on_string}"> | |
84 <filter>analysis['mode'] == 'c-alpha' and analysis['save_tscores']</filter> | |
85 </data> | |
60 </outputs> | 86 </outputs> |
61 <tests> | 87 <tests> |
62 <test> | 88 <test expect_num_outputs="1"> |
63 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" /> | 89 <!-- test counts mode with defaults --> |
64 <param name="controls" value="M10475 M10478" /> | 90 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
65 <param name="cases" value="M10500 M128215" /> | 91 <conditional name="analysis"> |
66 <param name="calpha" value="True" /> | 92 <param name="mode" value="counts" /> |
67 <output name="outfile" file="gemini_burden_result.tabular" /> | 93 </conditional> |
94 <output name="outfile" file="gemini_burden_count_highimpact_result.tabular" /> | |
95 </test> | |
96 <test expect_num_outputs="1"> | |
97 <!-- test nonsynonymous parameter --> | |
98 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> | |
99 <param name="nonsynonymous" value="--nonsynonymous" /> | |
100 <conditional name="analysis"> | |
101 <param name="mode" value="counts" /> | |
102 </conditional> | |
103 <output name="outfile" file="gemini_burden_count_nonsynonymous_result.tabular" /> | |
104 </test> | |
105 <test expect_num_outputs="1"> | |
106 <!-- test c-alpha mode with defaults --> | |
107 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> | |
108 <conditional name="analysis"> | |
109 <param name="mode" value="c-alpha" /> | |
110 <conditional name="casecontrol"> | |
111 <param name="source" value="ped" /> | |
112 </conditional> | |
113 </conditional> | |
114 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" /> | |
115 </test> | |
116 <test expect_num_outputs="1"> | |
117 <!-- test c-alpha mode with user-supplied case/control samples --> | |
118 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> | |
119 <conditional name="analysis"> | |
120 <param name="mode" value="c-alpha" /> | |
121 <conditional name="casecontrol"> | |
122 <param name="source" value="custom" /> | |
123 <param name="controls" value="1_kid 3_kid" /> | |
124 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" /> | |
125 </conditional> | |
126 </conditional> | |
127 <output name="outfile" file="gemini_burden_calpha_template.tabular" compare="re_match" /> | |
128 </test> | |
129 <test expect_num_outputs="2"> | |
130 <!-- test additional T scores output generation --> | |
131 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> | |
132 <conditional name="analysis"> | |
133 <param name="mode" value="c-alpha" /> | |
134 <conditional name="casecontrol"> | |
135 <param name="source" value="custom" /> | |
136 <param name="controls" value="1_kid 3_kid" /> | |
137 <param name="cases" value="1_dad 1_mom 3_dad 3_mom" /> | |
138 </conditional> | |
139 <param name="permutations" value="2" /> | |
140 <param name="save_tscores" value="True" /> | |
141 </conditional> | |
142 <output name="t_scores"> | |
143 <assert_contents> | |
144 <has_line_matching expression="WDR37	.+	.+" /> | |
145 </assert_contents> | |
146 </output> | |
68 </test> | 147 </test> |
69 </tests> | 148 </tests> |
70 <help><![CDATA[ | 149 <help><![CDATA[ |
71 **What it does** | 150 **What it does** |
72 | 151 |