|
18
|
1 <tool id="Tassel" name="Tassel" version="3.0.0">
|
|
9
|
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>
|
|
17
|
10 <command>
|
|
|
11 #if $analysis_opts.fonction_selector == "ck":
|
|
18
|
12 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
|
|
17
|
13 #else if $analysis_opts.fonction_selector == "ld":
|
|
18
|
14 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
|
|
9
|
15 #else if $analysis_opts.fonction_selector == "glm":
|
|
17
|
16 #if $analysis_opts.add_file.additional_file_selector == "no":
|
|
18
|
17 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
|
|
17
|
18 #else if $analysis_opts.add_file.additional_file_selector == "yes":
|
|
18
|
19 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
|
|
9
|
20 #end if
|
|
17
|
21 #else if $analysis_opts.fonction_selector == "mlm":
|
|
|
22 #if $analysis_opts.add_structure_file.additional_file_selector == "no":
|
|
18
|
23 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
|
|
17
|
24 #else if $analysis_opts.add_structure_file.additional_file_selector == "yes":
|
|
18
|
25 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
|
|
17
|
26 #end if
|
|
9
|
27 #end if
|
|
11
|
28 </command>
|
|
9
|
29 <inputs>
|
|
18
|
30 <param format="vcf" name="vcffile" type="data" label="VCF file"/>
|
|
9
|
31 <conditional name="analysis_opts">
|
|
|
32 <param name="fonction_selector" type="select" label="Type of analysis">
|
|
|
33 <option value="mlm" selected="True">MLM</option>
|
|
|
34 <option value="glm">GLM</option>
|
|
|
35 <option value="ld">Linkage Disequilibrium</option>
|
|
|
36 <option value="ck">Kinship</option>
|
|
|
37 </param>
|
|
|
38 <when value="glm">
|
|
|
39 <param format="txt" name="trait" type="data" label="Trait file"/>
|
|
|
40 <conditional name="add_file">
|
|
|
41 <param name="additional_file_selector" type="select" label="Add structure file">
|
|
|
42 <option value="no" selected="True">no</option>
|
|
|
43 <option value="yes">yes</option>
|
|
|
44 </param>
|
|
|
45 <when value="yes">
|
|
|
46 <param format="txt" name="structure" type="data" label="Structure file"/>
|
|
|
47 </when>
|
|
|
48 <when value="no">
|
|
|
49 </when>
|
|
|
50 </conditional>
|
|
|
51 </when>
|
|
|
52 <when value="mlm">
|
|
|
53 <param format="txt" name="trait" type="data" label="Trait file"/>
|
|
|
54 <param format="txt" name="kinship" type="data" label="Kinship file"/>
|
|
|
55 <conditional name="add_structure_file">
|
|
|
56 <param name="additional_file_selector" type="select" label="Add structure file">
|
|
|
57 <option value="no" selected="True">no</option>
|
|
|
58 <option value="yes">yes</option>
|
|
|
59 </param>
|
|
|
60 <when value="yes">
|
|
|
61 <param format="txt" name="structure" type="data" label="Structure file"/>
|
|
|
62 </when>
|
|
|
63 <when value="no">
|
|
|
64 </when>
|
|
|
65 </conditional>
|
|
|
66 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
|
|
|
67 <option value="P3D" selected="True">P3D</option>
|
|
|
68 <option value="EachMarker">EachMarker</option>
|
|
|
69 </param>
|
|
|
70 <param name="mlmCompressionLevel" type="select" label="Compression Level">
|
|
|
71 <option value="Optimum" selected="True">Optimum</option>
|
|
|
72 <option value="Custom">Custom</option>
|
|
|
73 <option value="None">None</option>
|
|
|
74 </param>
|
|
|
75 </when>
|
|
|
76 <when value="ld"></when>
|
|
|
77 <when value="ck"></when>
|
|
|
78 </conditional>
|
|
|
79 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
|
|
|
80 </inputs>
|
|
|
81 <outputs>
|
|
|
82 <data format="txt" name="output1" label="Tassel output">
|
|
|
83 <change_format>
|
|
|
84 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
|
|
|
85 </change_format>
|
|
|
86 </data>
|
|
|
87
|
|
|
88 <data format="txt" name="output2" label="Allele effects">
|
|
|
89 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
|
|
|
90 </data>
|
|
|
91
|
|
|
92 <data format="txt" name="output3" label="Compression file">
|
|
|
93 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
|
|
|
94 </data>
|
|
|
95
|
|
|
96 <data format="txt" name="log" label="Log file"/>
|
|
|
97 </outputs>
|
|
|
98 <tests>
|
|
|
99 <test>
|
|
18
|
100 <param name="vcffile" value="input.vcf"/>
|
|
9
|
101 <conditional name="analysis_opts">
|
|
|
102 <param name="fonction_selector" value="glm"/>
|
|
18
|
103 <param name="trait" value="phenotyping_xantho.tsv"/>
|
|
9
|
104 <conditional name="add_structure_file">
|
|
|
105 <param name="additional_file_selector" value="yes"/>
|
|
18
|
106 <param name="structure" value="Best_K_Output2"/>
|
|
9
|
107 </conditional>
|
|
|
108 </conditional>
|
|
|
109 <param name="filterAlignMinFreq" value="0.05"/>
|
|
18
|
110 <output name="output1" value="statistics_output.txt"/>
|
|
|
111 <output name="output2" value="Allele_effects_output.txt"/>
|
|
9
|
112 </test>
|
|
|
113 </tests>
|
|
|
114 <help><![CDATA[
|
|
13
|
115 .. class:: infomark
|
|
|
116
|
|
|
117 **Tassel5** version 5.2.40
|
|
|
118
|
|
|
119 .. class:: infomark
|
|
|
120
|
|
|
121 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
|
|
|
122
|
|
|
123 .. class:: infomark
|
|
|
124
|
|
|
125 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
|
|
|
126
|
|
|
127 ---------------------------------------------------
|
|
|
128
|
|
|
129 =======
|
|
|
130 Tassel5
|
|
|
131 =======
|
|
|
132
|
|
|
133 -----------
|
|
|
134 Description
|
|
|
135 -----------
|
|
|
136
|
|
|
137 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
|
|
|
138 | For further informations on tassel, please visit the website_.
|
|
|
139
|
|
|
140 .. _website: http://www.maizegenetics.net/tassel/
|
|
|
141
|
|
|
142 ------------
|
|
|
143 Dependencies
|
|
|
144 ------------
|
|
|
145
|
|
|
146 Tassel5
|
|
|
147
|
|
|
148 tassel_ 5.2.40, Conda version
|
|
|
149
|
|
|
150 .. _tassel: https://anaconda.org/bioconda/tassel
|
|
|
151
|
|
9
|
152 ]]></help>
|
|
|
153 <citations>
|
|
|
154 <citation type="doi">10.1093/bioinformatics/btm308</citation>
|
|
|
155 </citations>
|
|
13
|
156 </tool>
|
