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comparison tassel.xml @ 4:652aafd88060 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:54:41 -0400
parents 0eebff4180d9
children 28c0efb3a226
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3:0eebff4180d9 4:652aafd88060
1 <tool id="Tassel" name="Tassel" version="5.0"> 1 <tool id="Tassel" name="Tassel" version="2.0.0">
2 <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description> 2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.0">tassel</requirement> 4 <requirement type="package" version="5.2.40">tassel</requirement>
5 </requirements> 5 </requirements>
6
7 <stdio>
8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
9 <exit_code range="1:" level="fatal" />
10 </stdio>
11
6 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ 12 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
7 #if $analysis_opts.fonction_selector == "mlm": 13 #if $analysis_opts.fonction_selector == "mlm":
8 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq 14 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
9 -fork2 -r $analysis_opts.trait 15 -fork2 -r $analysis_opts.trait
10 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 16 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
60 <option value="yes">yes</option> 66 <option value="yes">yes</option>
61 </param> 67 </param>
62 <when value="yes"> 68 <when value="yes">
63 <param format="txt" name="structure" type="data" label="Structure file"/> 69 <param format="txt" name="structure" type="data" label="Structure file"/>
64 </when> 70 </when>
71 <when value="no">
72 </when>
65 </conditional> 73 </conditional>
66 </when> 74 </when>
67 <when value="mlm"> 75 <when value="mlm">
68 <param format="txt" name="trait" type="data" label="Trait file"/> 76 <param format="txt" name="trait" type="data" label="Trait file"/>
69 <param format="txt" name="kinship" type="data" label="Kinship file"/> 77 <param format="txt" name="kinship" type="data" label="Kinship file"/>
73 <option value="yes">yes</option> 81 <option value="yes">yes</option>
74 </param> 82 </param>
75 <when value="yes"> 83 <when value="yes">
76 <param format="txt" name="structure" type="data" label="Structure file"/> 84 <param format="txt" name="structure" type="data" label="Structure file"/>
77 </when> 85 </when>
86 <when value="no">
87 </when>
78 </conditional> 88 </conditional>
79 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation"> 89 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
80 <option value="P3D" selected="True">P3D</option> 90 <option value="P3D" selected="True">P3D</option>
81 <option value="EachMarker">EachMarker</option> 91 <option value="EachMarker">EachMarker</option>
82 </param> 92 </param>
106 <filter>analysis_opts['fonction_selector'] == "mlm"</filter> 116 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
107 </data> 117 </data>
108 118
109 <data format="txt" name="log" label="Log file"/> 119 <data format="txt" name="log" label="Log file"/>
110 </outputs> 120 </outputs>
111 <help> 121
122 <tests>
123 <test>
124 <param name="hapmap" value="input_hapmap.txt"/>
125 <conditional name="analysis_opts">
126 <param name="fonction_selector" value="glm"/>
127 <param name="trait" value="phenotyping_DRB.csv"/>
128 <conditional name="add_structure_file">
129 <param name="additional_file_selector" value="yes"/>
130 <param name="structure" value="Best_K_Output"/>
131 </conditional>
132 </conditional>
133 <param name="filterAlignMinFreq" value="0.05"/>
134 <output name="output1" value="Tassel_output.txt"/>
135 <output name="output2" value="Allele_effects.txt"/>
136 </test>
137 </tests>
138
139 <help><![CDATA[
140
112 141
113 .. class:: infomark 142 .. class:: infomark
114 143
115 **Program encapsulated in Galaxy by Southgreen** 144 **Tassel5** version 5.2.40
116 145
117 .. class:: infomark 146 .. class:: infomark
118 147
119 **Tassel** 148 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
120 149
121 ----- 150 .. class:: infomark
122 151
123 ========== 152 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
124 Authors:
125 ==========
126 153
127 **Terry Casstevens** 154 ---------------------------------------------------
128 155
129 ----- 156 =======
157 Tassel5
158 =======
130 159
131 ========== 160 -----------
132 Overview 161 Description
133 ========== 162 -----------
134 163
135 Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. 164 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
165 | For further informations on tassel, please visit the website_.
136 166
137 ----- 167 .. _website: http://www.maizegenetics.net/tassel/
138 168
139 For further informations, please visite the website of TASSEL_. 169 ------------
170 Dependencies
171 ------------
172 Tassel5
173 tassel_ 5.2.40, Conda version
140 174
175 .. _tassel: https://anaconda.org/bioconda/tassel
141 176
142 .. _TASSEL: http://www.maizegenetics.net/tassel/ 177 ]]></help>
143 178 <citations>
144 </help> 179 <citation type="doi">10.1093/bioinformatics/btm308</citation>
145 <!-- 180 </citations>
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> 181 </tool>