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comparison old_version/optimizer.xml @ 2:6e4eb4856874 draft

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author elixir-it
date Wed, 22 Jul 2020 19:20:30 +0000
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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>