Mercurial > repos > dereeper > tassel5
comparison tassel/tassel.xml @ 0:0aeea77b924a draft
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author | dereeper |
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date | Thu, 26 Feb 2015 01:15:36 -0500 |
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children | 1dc58d808e72 |
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1 <tool id="Tassel" name="Tassel"> | |
2 <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description> | |
3 <!--<command interpreter="bash"> | |
4 ./tassel.sh $hapmap $trait $structure $filter $output1 $output2 $log | |
5 </command> | |
6 --> | |
7 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ | |
8 #if $analysis_opts.fonction_selector == "mlm": | |
9 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq | |
10 -fork2 -r $analysis_opts.trait | |
11 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": | |
12 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait | |
13 #end if | |
14 -fork4 -k $analysis_opts.kinship | |
15 -combineA -input1 -input2 | |
16 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": | |
17 -input3 | |
18 #end if | |
19 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 | |
20 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": | |
21 -runfork3 | |
22 #end if | |
23 -runfork4 | |
24 | |
25 #else if $analysis_opts.fonction_selector == "glm": | |
26 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq | |
27 -fork2 -r $analysis_opts.trait | |
28 #if $analysis_opts.add_file.additional_file_selector == "yes": | |
29 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait | |
30 #end if | |
31 -combineA -input1 -input2 | |
32 #if $analysis_opts.add_file.additional_file_selector == "yes": | |
33 -input3 | |
34 #end if | |
35 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2 | |
36 #if $analysis_opts.add_file.additional_file_selector == "yes": | |
37 -runfork3 | |
38 #end if | |
39 #else if $analysis_opts.fonction_selector == "ld": | |
40 -fork1 -h $hapmap | |
41 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1 | |
42 #else if $analysis_opts.fonction_selector == "ck": | |
43 -fork1 -h $hapmap | |
44 -ck -export tmpdir$$/kinship -runfork1 | |
45 #end if | |
46 </command> | |
47 <inputs> | |
48 <param format="txt" name="hapmap" type="data" label="HapMap file"/> | |
49 <conditional name="analysis_opts"> | |
50 <param name="fonction_selector" type="select" label="Type of analysis"> | |
51 <option value="mlm" selected="True">MLM</option> | |
52 <option value="glm">GLM</option> | |
53 <option value="ld">Linkage Disequilibrium</option> | |
54 <option value="ck">Kinship</option> | |
55 </param> | |
56 <when value="glm"> | |
57 <param format="txt" name="trait" type="data" label="Trait file"/> | |
58 <conditional name="add_file"> | |
59 <param name="additional_file_selector" type="select" label="Add structure file"> | |
60 <option value="no" selected="True">no</option> | |
61 <option value="yes">yes</option> | |
62 </param> | |
63 <when value="yes"> | |
64 <param format="txt" name="structure" type="data" label="Structure file"/> | |
65 </when> | |
66 </conditional> | |
67 </when> | |
68 <when value="mlm"> | |
69 <param format="txt" name="trait" type="data" label="Trait file"/> | |
70 <param format="txt" name="kinship" type="data" label="Kinship file"/> | |
71 <conditional name="add_structure_file"> | |
72 <param name="additional_file_selector" type="select" label="Add structure file"> | |
73 <option value="no" selected="True">no</option> | |
74 <option value="yes">yes</option> | |
75 </param> | |
76 <when value="yes"> | |
77 <param format="txt" name="structure" type="data" label="Structure file"/> | |
78 </when> | |
79 </conditional> | |
80 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation"> | |
81 <option value="P3D" selected="True">P3D</option> | |
82 <option value="EachMarker">EachMarker</option> | |
83 </param> | |
84 <param name="mlmCompressionLevel" type="select" label="Compression Level"> | |
85 <option value="Optimum" selected="True">Optimum</option> | |
86 <option value="Custom">Custom</option> | |
87 <option value="None">None</option> | |
88 </param> | |
89 </when> | |
90 <when value="ld"></when> | |
91 <when value="ck"></when> | |
92 </conditional> | |
93 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/> | |
94 </inputs> | |
95 <outputs> | |
96 <data format="txt" name="output1" label="Tassel output"> | |
97 <change_format> | |
98 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/> | |
99 </change_format> | |
100 </data> | |
101 | |
102 <data format="txt" name="output2" label="Allele effects"> | |
103 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter> | |
104 </data> | |
105 | |
106 <data format="txt" name="output3" label="Compression file"> | |
107 <filter>analysis_opts['fonction_selector'] == "mlm"</filter> | |
108 </data> | |
109 | |
110 <data format="txt" name="log" label="Log file"/> | |
111 </outputs> | |
112 <help> | |
113 | |
114 .. class:: infomark | |
115 | |
116 **Program encapsulated in Galaxy by Southgreen** | |
117 | |
118 .. class:: infomark | |
119 | |
120 **Tassel** | |
121 | |
122 ----- | |
123 | |
124 ========== | |
125 Authors: | |
126 ========== | |
127 | |
128 **Terry Casstevens** | |
129 | |
130 ----- | |
131 | |
132 ========== | |
133 Overview | |
134 ========== | |
135 | |
136 Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. | |
137 | |
138 ----- | |
139 | |
140 For further informations, please visite the website of TASSEL_. | |
141 | |
142 | |
143 .. _TASSEL: http://www.maizegenetics.net/tassel/ | |
144 | |
145 </help> | |
146 <!-- | |
147 <tests> | |
148 <test> | |
149 <param name="input" value="genotyping_file.inp" /> | |
150 <output name="output" file="phase_output" /> | |
151 </test> | |
152 </tests> | |
153 --> | |
154 </tool> |