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comparison tassel.xml @ 3:0eebff4180d9 draft

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author dereeper
date Thu, 02 Nov 2017 05:19:30 -0400
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1 <tool id="Tassel" name="Tassel" version="5.0">
2 <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
3 <requirements>
4 <requirement type="package" version="5.0">tassel</requirement>
5 </requirements>
6 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
7 #if $analysis_opts.fonction_selector == "mlm":
8 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
9 -fork2 -r $analysis_opts.trait
10 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
11 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
12 #end if
13 -fork4 -k $analysis_opts.kinship
14 -combineA -input1 -input2
15 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
16 -input3
17 #end if
18 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
19 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
20 -runfork3
21 #end if
22 -runfork4
23
24 #else if $analysis_opts.fonction_selector == "glm":
25 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
26 -fork2 -r $analysis_opts.trait
27 #if $analysis_opts.add_file.additional_file_selector == "yes":
28 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
29 #end if
30 -combineA -input1 -input2
31 #if $analysis_opts.add_file.additional_file_selector == "yes":
32 -input3
33 #end if
34 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
35 #if $analysis_opts.add_file.additional_file_selector == "yes":
36 -runfork3
37 #end if
38 #else if $analysis_opts.fonction_selector == "ld":
39 -fork1 -h $hapmap
40 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
41 #else if $analysis_opts.fonction_selector == "ck":
42 -fork1 -h $hapmap
43 -ck -export tmpdir$$/kinship -runfork1
44 #end if
45 </command>
46 <inputs>
47 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
48 <conditional name="analysis_opts">
49 <param name="fonction_selector" type="select" label="Type of analysis">
50 <option value="mlm" selected="True">MLM</option>
51 <option value="glm">GLM</option>
52 <option value="ld">Linkage Disequilibrium</option>
53 <option value="ck">Kinship</option>
54 </param>
55 <when value="glm">
56 <param format="txt" name="trait" type="data" label="Trait file"/>
57 <conditional name="add_file">
58 <param name="additional_file_selector" type="select" label="Add structure file">
59 <option value="no" selected="True">no</option>
60 <option value="yes">yes</option>
61 </param>
62 <when value="yes">
63 <param format="txt" name="structure" type="data" label="Structure file"/>
64 </when>
65 </conditional>
66 </when>
67 <when value="mlm">
68 <param format="txt" name="trait" type="data" label="Trait file"/>
69 <param format="txt" name="kinship" type="data" label="Kinship file"/>
70 <conditional name="add_structure_file">
71 <param name="additional_file_selector" type="select" label="Add structure file">
72 <option value="no" selected="True">no</option>
73 <option value="yes">yes</option>
74 </param>
75 <when value="yes">
76 <param format="txt" name="structure" type="data" label="Structure file"/>
77 </when>
78 </conditional>
79 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
80 <option value="P3D" selected="True">P3D</option>
81 <option value="EachMarker">EachMarker</option>
82 </param>
83 <param name="mlmCompressionLevel" type="select" label="Compression Level">
84 <option value="Optimum" selected="True">Optimum</option>
85 <option value="Custom">Custom</option>
86 <option value="None">None</option>
87 </param>
88 </when>
89 <when value="ld"></when>
90 <when value="ck"></when>
91 </conditional>
92 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
93 </inputs>
94 <outputs>
95 <data format="txt" name="output1" label="Tassel output">
96 <change_format>
97 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
98 </change_format>
99 </data>
100
101 <data format="txt" name="output2" label="Allele effects">
102 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
103 </data>
104
105 <data format="txt" name="output3" label="Compression file">
106 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
107 </data>
108
109 <data format="txt" name="log" label="Log file"/>
110 </outputs>
111 <help>
112
113 .. class:: infomark
114
115 **Program encapsulated in Galaxy by Southgreen**
116
117 .. class:: infomark
118
119 **Tassel**
120
121 -----
122
123 ==========
124 Authors:
125 ==========
126
127 **Terry Casstevens**
128
129 -----
130
131 ==========
132 Overview
133 ==========
134
135 Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
136
137 -----
138
139 For further informations, please visite the website of TASSEL_.
140
141
142 .. _TASSEL: http://www.maizegenetics.net/tassel/
143
144 </help>
145 <!--
146 <tests>
147 <test>
148 <param name="input" value="genotyping_file.inp" />
149 <output name="output" file="phase_output" />
150 </test>
151 </tests>
152 -->
153 </tool>