|
9
|
1 <tool id="Tassel" name="Tassel" version="2.0.0">
|
|
|
2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
|
|
|
3 <requirements>
|
|
15
|
4 <requirement type="package" version="5.2.89">tassel</requirement>
|
|
9
|
5 </requirements>
|
|
|
6 <stdio>
|
|
|
7 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
|
|
|
8 <exit_code range="1:" level="fatal" />
|
|
|
9 </stdio>
|
|
15
|
10 <command>$__tool_directory__/tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
|
|
9
|
11 #if $analysis_opts.fonction_selector == "mlm":
|
|
|
12 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
|
|
|
13 -fork2 -r $analysis_opts.trait
|
|
|
14 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
|
|
|
15 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
|
|
|
16 #end if
|
|
|
17 -fork4 -k $analysis_opts.kinship
|
|
|
18 -combineA -input1 -input2
|
|
|
19 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
|
|
|
20 -input3
|
|
|
21 #end if
|
|
|
22 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
|
|
|
23 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
|
|
|
24 -runfork3
|
|
|
25 #end if
|
|
|
26 -runfork4
|
|
|
27
|
|
|
28 #else if $analysis_opts.fonction_selector == "glm":
|
|
|
29 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
|
|
|
30 -fork2 -r $analysis_opts.trait
|
|
|
31 #if $analysis_opts.add_file.additional_file_selector == "yes":
|
|
|
32 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
|
|
|
33 #end if
|
|
|
34 -combineA -input1 -input2
|
|
|
35 #if $analysis_opts.add_file.additional_file_selector == "yes":
|
|
|
36 -input3
|
|
|
37 #end if
|
|
|
38 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
|
|
|
39 #if $analysis_opts.add_file.additional_file_selector == "yes":
|
|
|
40 -runfork3
|
|
|
41 #end if
|
|
|
42 #else if $analysis_opts.fonction_selector == "ld":
|
|
|
43 -fork1 -h $hapmap
|
|
|
44 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
|
|
|
45 #else if $analysis_opts.fonction_selector == "ck":
|
|
|
46 -fork1 -h $hapmap
|
|
|
47 -ck -export tmpdir$$/kinship -runfork1
|
|
|
48 #end if
|
|
11
|
49 </command>
|
|
9
|
50 <inputs>
|
|
|
51 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
|
|
|
52 <conditional name="analysis_opts">
|
|
|
53 <param name="fonction_selector" type="select" label="Type of analysis">
|
|
|
54 <option value="mlm" selected="True">MLM</option>
|
|
|
55 <option value="glm">GLM</option>
|
|
|
56 <option value="ld">Linkage Disequilibrium</option>
|
|
|
57 <option value="ck">Kinship</option>
|
|
|
58 </param>
|
|
|
59 <when value="glm">
|
|
|
60 <param format="txt" name="trait" type="data" label="Trait file"/>
|
|
|
61 <conditional name="add_file">
|
|
|
62 <param name="additional_file_selector" type="select" label="Add structure file">
|
|
|
63 <option value="no" selected="True">no</option>
|
|
|
64 <option value="yes">yes</option>
|
|
|
65 </param>
|
|
|
66 <when value="yes">
|
|
|
67 <param format="txt" name="structure" type="data" label="Structure file"/>
|
|
|
68 </when>
|
|
|
69 <when value="no">
|
|
|
70 </when>
|
|
|
71 </conditional>
|
|
|
72 </when>
|
|
|
73 <when value="mlm">
|
|
|
74 <param format="txt" name="trait" type="data" label="Trait file"/>
|
|
|
75 <param format="txt" name="kinship" type="data" label="Kinship file"/>
|
|
|
76 <conditional name="add_structure_file">
|
|
|
77 <param name="additional_file_selector" type="select" label="Add structure file">
|
|
|
78 <option value="no" selected="True">no</option>
|
|
|
79 <option value="yes">yes</option>
|
|
|
80 </param>
|
|
|
81 <when value="yes">
|
|
|
82 <param format="txt" name="structure" type="data" label="Structure file"/>
|
|
|
83 </when>
|
|
|
84 <when value="no">
|
|
|
85 </when>
|
|
|
86 </conditional>
|
|
|
87 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
|
|
|
88 <option value="P3D" selected="True">P3D</option>
|
|
|
89 <option value="EachMarker">EachMarker</option>
|
|
|
90 </param>
|
|
|
91 <param name="mlmCompressionLevel" type="select" label="Compression Level">
|
|
|
92 <option value="Optimum" selected="True">Optimum</option>
|
|
|
93 <option value="Custom">Custom</option>
|
|
|
94 <option value="None">None</option>
|
|
|
95 </param>
|
|
|
96 </when>
|
|
|
97 <when value="ld"></when>
|
|
|
98 <when value="ck"></when>
|
|
|
99 </conditional>
|
|
|
100 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
|
|
|
101 </inputs>
|
|
|
102 <outputs>
|
|
|
103 <data format="txt" name="output1" label="Tassel output">
|
|
|
104 <change_format>
|
|
|
105 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
|
|
|
106 </change_format>
|
|
|
107 </data>
|
|
|
108
|
|
|
109 <data format="txt" name="output2" label="Allele effects">
|
|
|
110 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
|
|
|
111 </data>
|
|
|
112
|
|
|
113 <data format="txt" name="output3" label="Compression file">
|
|
|
114 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
|
|
|
115 </data>
|
|
|
116
|
|
|
117 <data format="txt" name="log" label="Log file"/>
|
|
|
118 </outputs>
|
|
|
119
|
|
|
120 <tests>
|
|
|
121 <test>
|
|
|
122 <param name="hapmap" value="input_hapmap.txt"/>
|
|
|
123 <conditional name="analysis_opts">
|
|
|
124 <param name="fonction_selector" value="glm"/>
|
|
|
125 <param name="trait" value="phenotyping_DRB.csv"/>
|
|
|
126 <conditional name="add_structure_file">
|
|
|
127 <param name="additional_file_selector" value="yes"/>
|
|
|
128 <param name="structure" value="Best_K_Output"/>
|
|
|
129 </conditional>
|
|
|
130 </conditional>
|
|
|
131 <param name="filterAlignMinFreq" value="0.05"/>
|
|
|
132 <output name="output1" value="Tassel_output.txt"/>
|
|
|
133 <output name="output2" value="Allele_effects.txt"/>
|
|
|
134 </test>
|
|
|
135 </tests>
|
|
|
136 <help><![CDATA[
|
|
13
|
137 .. class:: infomark
|
|
|
138
|
|
|
139 **Tassel5** version 5.2.40
|
|
|
140
|
|
|
141 .. class:: infomark
|
|
|
142
|
|
|
143 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
|
|
|
144
|
|
|
145 .. class:: infomark
|
|
|
146
|
|
|
147 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
|
|
|
148
|
|
|
149 ---------------------------------------------------
|
|
|
150
|
|
|
151 =======
|
|
|
152 Tassel5
|
|
|
153 =======
|
|
|
154
|
|
|
155 -----------
|
|
|
156 Description
|
|
|
157 -----------
|
|
|
158
|
|
|
159 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
|
|
|
160 | For further informations on tassel, please visit the website_.
|
|
|
161
|
|
|
162 .. _website: http://www.maizegenetics.net/tassel/
|
|
|
163
|
|
|
164 ------------
|
|
|
165 Dependencies
|
|
|
166 ------------
|
|
|
167
|
|
|
168 Tassel5
|
|
|
169
|
|
|
170 tassel_ 5.2.40, Conda version
|
|
|
171
|
|
|
172 .. _tassel: https://anaconda.org/bioconda/tassel
|
|
|
173
|
|
9
|
174 ]]></help>
|
|
|
175 <citations>
|
|
|
176 <citation type="doi">10.1093/bioinformatics/btm308</citation>
|
|
|
177 </citations>
|
|
13
|
178 </tool>
|
