|
2
|
1 <tool id="optimizer" name="optimizer" version="1">
|
|
|
2 <description> Optimizer</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" >perl</requirement>
|
|
|
5 <requirement type="package" >r-base</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command> <![CDATA[
|
|
|
8 ln -s $__tool_directory__/score_complete_alt.pl 2>$log &&
|
|
|
9 ln -s $__tool_directory__/wilcox.R 2>>$log &&
|
|
|
10 ln -s $fileR fileR &&
|
|
|
11 ln -s $fileC fileC &&
|
|
|
12
|
|
|
13
|
|
|
14
|
|
|
15
|
|
|
16 perl $__tool_directory__/optimizer.pl
|
|
|
17
|
|
|
18
|
|
|
19 ###INPUT VCF FILE
|
|
|
20
|
|
|
21 -fileR fileR -fileC fileC
|
|
|
22
|
|
|
23
|
|
|
24
|
|
|
25
|
|
|
26 #if $qfile
|
|
|
27 -leQTL $qfile
|
|
|
28 #else
|
|
|
29 -leQTL $__tool_directory__/qfile
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #if $similarD
|
|
|
33 -similarD $similarD
|
|
|
34 #end if
|
|
|
35
|
|
|
36 #if $disease
|
|
|
37 -disease $disease
|
|
|
38 #end if
|
|
|
39
|
|
|
40 #if $lgenes
|
|
|
41 -lgenes $lgenes
|
|
|
42 #end if
|
|
|
43
|
|
|
44 #if $kfile
|
|
|
45 -keywords $kfile
|
|
|
46 #else
|
|
|
47 -keywords $__tool_directory__/kfile
|
|
|
48 #end if
|
|
|
49
|
|
|
50 #if $efile
|
|
|
51 -effects $efile
|
|
|
52 #else
|
|
|
53 -effects $__tool_directory__/efile
|
|
|
54 #end if
|
|
|
55
|
|
|
56
|
|
|
57 ###RANGE VALUES
|
|
|
58 -disease_clinvar $disease_clinvarMIN:$disease_clinvarMAX
|
|
|
59
|
|
|
60 -score_AF $score_AFMIN:$score_AFMAX
|
|
|
61
|
|
|
62 -score_functional $score_functionalMIN:$score_functionalMAX
|
|
|
63
|
|
|
64 -score_NS $score_NSMIN:$score_NSMAX
|
|
|
65
|
|
|
66 -score_nIND $score_nINDMIN:$score_nINDMAX
|
|
|
67
|
|
|
68 -AF $AF
|
|
|
69
|
|
|
70 -scoreeQTL $scoreeQTLMIN:$scoreeQTLMAX
|
|
|
71
|
|
|
72 -scoreG $scoreGMIN:$scoreGMAX
|
|
|
73 -nind $nind
|
|
|
74
|
|
|
75 ###OUTPUT
|
|
|
76 -ofile $ofile
|
|
|
77
|
|
|
78 2>>$log
|
|
|
79
|
|
|
80
|
|
|
81
|
|
|
82 ]]>
|
|
|
83 </command>
|
|
|
84 <inputs>
|
|
|
85 <param format="vcf" name="fileR" type="data" label="VCF" help="vcf fileR test ALL input file"/>
|
|
|
86 <param format="vcf" name="fileC" type="data" label="VCF" help="vcf fileC test test_unefected input file"/>
|
|
|
87 <!-- default values-->
|
|
|
88 <param name="disease_clinvarMIN" value="4" type="integer"/>
|
|
|
89 <param name="disease_clinvarMAX" value="6" type="integer"/>
|
|
|
90 <param name="score_AFMIN" value="2" type="integer"/>
|
|
|
91 <param name="score_AFMAX" value="4" type="integer"/>
|
|
|
92 <param name="score_functionalMIN" value="4" type="integer"/>
|
|
|
93 <param name="score_functionalMAX" value="6" type="integer"/>
|
|
|
94 <param name="score_NSMIN" value="2" type="integer"/>
|
|
|
95 <param name="score_NSMAX" value="4" type="integer"/>
|
|
|
96 <param name="score_nINDMIN" value="2" type="integer"/>
|
|
|
97 <param name="score_nINDMAX" value="4" type="integer"/>
|
|
|
98 <param name="AF" value="0.0001" type="float"/>
|
|
|
99 <param name="scoreeQTLMIN" value="2" type="integer"/>
|
|
|
100 <param name="scoreeQTLMAX" value="4" type="integer"/>
|
|
|
101 <param name="nind" value="5" min="5" type="integer"/>
|
|
|
102 <param name="scoreGMIN" value="3" type="integer"/>
|
|
|
103 <param name="scoreGMAX" value="5" type="integer"/>
|
|
|
104 <!--optional values -->
|
|
|
105 <param format="txt" name="kfile" type="data" optional="true" label="txt kfile" help="input kfile"/>
|
|
|
106 <param format="txt" name="efile" type="data" optional="true" label="txt efile" help="input efile"/>
|
|
|
107 <param format="txt" name="qfile" type="data" optional="true" label="txt qfile" help="input qfile"/>
|
|
|
108 <param name="disease" type="text" optional="true"/>
|
|
|
109 <param name="similarD" type="data" format="txt" optional="true"/>
|
|
|
110 <param name="lgenes" type="data" format="txt" optional="true"/>
|
|
|
111 <!--others-->
|
|
|
112
|
|
|
113 </inputs>
|
|
|
114 <outputs>
|
|
|
115 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
|
|
|
116 <data format="tabular" name="ofile" label="${tool.name} on ${on_string}: tabular "/>
|
|
|
117 </outputs>
|
|
|
118 <stdio>
|
|
|
119 </stdio>
|
|
|
120 <tests>
|
|
|
121 <test>
|
|
|
122 </test>
|
|
|
123 </tests>
|
|
|
124 <help>
|
|
|
125 **What it does**
|
|
|
126
|
|
|
127
|
|
|
128
|
|
|
129 **Important Usage Note**
|
|
|
130
|
|
|
131
|
|
|
132
|
|
|
133 </help>
|
|
|
134 <citations>
|
|
|
135 </citations>
|
|
|
136 </tool>
|
