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comparison tassel.xml @ 9:b2f196d098cb draft

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author dereeper
date Wed, 03 Jan 2024 09:30:12 +0000
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8:7ec8715bedc2 9:b2f196d098cb
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>
4 <requirement type="package" version="5.2.89">tassel</requirement>
5 <requirement type="package" version="1.8">openjdk</requirement>
6 </requirements>
7 ​
8 <stdio>
9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
10 <exit_code range="1:" level="fatal" />
11 </stdio>
12 ​
13 <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
14 #if $analysis_opts.fonction_selector == "mlm":
15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
16 -fork2 -r $analysis_opts.trait
17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
19 #end if
20 -fork4 -k $analysis_opts.kinship
21 -combineA -input1 -input2
22 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
23 -input3
24 #end if
25 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
26 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
27 -runfork3
28 #end if
29 -runfork4
30
31 #else if $analysis_opts.fonction_selector == "glm":
32 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
33 -fork2 -r $analysis_opts.trait
34 #if $analysis_opts.add_file.additional_file_selector == "yes":
35 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
36 #end if
37 -combineA -input1 -input2
38 #if $analysis_opts.add_file.additional_file_selector == "yes":
39 -input3
40 #end if
41 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
42 #if $analysis_opts.add_file.additional_file_selector == "yes":
43 -runfork3
44 #end if
45 #else if $analysis_opts.fonction_selector == "ld":
46 -fork1 -h $hapmap
47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
48 #else if $analysis_opts.fonction_selector == "ck":
49 -fork1 -h $hapmap
50 -ck -export tmpdir$$/kinship -runfork1
51 #end if
52 ]]></command>
53 <inputs>
54 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
55 <conditional name="analysis_opts">
56 <param name="fonction_selector" type="select" label="Type of analysis">
57 <option value="mlm" selected="True">MLM</option>
58 <option value="glm">GLM</option>
59 <option value="ld">Linkage Disequilibrium</option>
60 <option value="ck">Kinship</option>
61 </param>
62 <when value="glm">
63 <param format="txt" name="trait" type="data" label="Trait file"/>
64 <conditional name="add_file">
65 <param name="additional_file_selector" type="select" label="Add structure file">
66 <option value="no" selected="True">no</option>
67 <option value="yes">yes</option>
68 </param>
69 <when value="yes">
70 <param format="txt" name="structure" type="data" label="Structure file"/>
71 </when>
72 <when value="no">
73 </when>
74 </conditional>
75 </when>
76 <when value="mlm">
77 <param format="txt" name="trait" type="data" label="Trait file"/>
78 <param format="txt" name="kinship" type="data" label="Kinship file"/>
79 <conditional name="add_structure_file">
80 <param name="additional_file_selector" type="select" label="Add structure file">
81 <option value="no" selected="True">no</option>
82 <option value="yes">yes</option>
83 </param>
84 <when value="yes">
85 <param format="txt" name="structure" type="data" label="Structure file"/>
86 </when>
87 <when value="no">
88 </when>
89 </conditional>
90 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
91 <option value="P3D" selected="True">P3D</option>
92 <option value="EachMarker">EachMarker</option>
93 </param>
94 <param name="mlmCompressionLevel" type="select" label="Compression Level">
95 <option value="Optimum" selected="True">Optimum</option>
96 <option value="Custom">Custom</option>
97 <option value="None">None</option>
98 </param>
99 </when>
100 <when value="ld"></when>
101 <when value="ck"></when>
102 </conditional>
103 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
104 </inputs>
105 <outputs>
106 <data format="txt" name="output1" label="Tassel output">
107 <change_format>
108 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
109 </change_format>
110 </data>
111
112 <data format="txt" name="output2" label="Allele effects">
113 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
114 </data>
115
116 <data format="txt" name="output3" label="Compression file">
117 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
118 </data>
119
120 <data format="txt" name="log" label="Log file"/>
121 </outputs>
122 ​
123 <tests>
124 <test>
125 <param name="hapmap" value="input_hapmap.txt"/>
126 <conditional name="analysis_opts">
127 <param name="fonction_selector" value="glm"/>
128 <param name="trait" value="phenotyping_DRB.csv"/>
129 <conditional name="add_structure_file">
130 <param name="additional_file_selector" value="yes"/>
131 <param name="structure" value="Best_K_Output"/>
132 </conditional>
133 </conditional>
134 <param name="filterAlignMinFreq" value="0.05"/>
135 <output name="output1" value="Tassel_output.txt"/>
136 <output name="output2" value="Allele_effects.txt"/>
137 </test>
138 </tests>
139 ​
140 <help><![CDATA[
141 ​
142 ​
143 .. class:: infomark
144 ​
145 **Tassel5** version 5.2.40
146 ​
147 .. class:: infomark
148 ​
149 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
150 ​
151 .. class:: infomark
152 ​
153 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
154 ​
155 ---------------------------------------------------
156 ​
157 =======
158 Tassel5
159 =======
160 ​
161 -----------
162 Description
163 -----------
164 ​
165 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
166 | For further informations on tassel, please visit the website_.
167 ​
168 .. _website: http://www.maizegenetics.net/tassel/
169 ​
170 ------------
171 Dependencies
172 ------------
173 Tassel5
174 tassel_ 5.2.40, Conda version
175 ​
176 .. _tassel: https://anaconda.org/bioconda/tassel
177 ​
178 ]]></help>
179 <citations>
180 <citation type="doi">10.1093/bioinformatics/btm308</citation>
181 </citations>
182 </tool>