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comparison tassel.xml @ 13:a29a0f2c0897 draft

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author dereeper
date Mon, 15 Jan 2024 13:14:13 +0000
parents 4ca9252178df
children 5cd3fed90e93
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12:4ca9252178df 13:a29a0f2c0897
1 <tool id="Tassel" name="Tassel" version="2.0.0"> 1 <tool id="Tassel" name="Tassel" version="2.0.0">
2 <description>Software 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="5.2.89">tassel</requirement> 4 <requirement type="package" version="5.2.89">tassel</requirement>
5 <requirement type="package" version="8.0.302">openjdk</requirement>
6 </requirements> 5 </requirements>
7 ​
8 <stdio> 6 <stdio>
9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 7 <!-- [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" /> 8 <exit_code range="1:" level="fatal" />
11 </stdio> 9 </stdio>
12 ​
13 <command>tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ 10 <command>tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
14 #if $analysis_opts.fonction_selector == "mlm": 11 #if $analysis_opts.fonction_selector == "mlm":
15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq 12 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
16 -fork2 -r $analysis_opts.trait 13 -fork2 -r $analysis_opts.trait
17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 14 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
134 <param name="filterAlignMinFreq" value="0.05"/> 131 <param name="filterAlignMinFreq" value="0.05"/>
135 <output name="output1" value="Tassel_output.txt"/> 132 <output name="output1" value="Tassel_output.txt"/>
136 <output name="output2" value="Allele_effects.txt"/> 133 <output name="output2" value="Allele_effects.txt"/>
137 </test> 134 </test>
138 </tests> 135 </tests>
139 ​
140 <help><![CDATA[ 136 <help><![CDATA[
141 ​ 137 .. class:: infomark
142 ​ 138
143 .. class:: infomark 139 **Tassel5** version 5.2.40
144 ​ 140
145 **Tassel5** version 5.2.40 141 .. class:: infomark
146 ​ 142
147 .. class:: infomark 143 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
148 ​ 144
149 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) 145 .. class:: infomark
150 ​ 146
151 .. class:: infomark 147 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
152 ​ 148
153 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr 149 ---------------------------------------------------
154 ​ 150
155 --------------------------------------------------- 151 =======
156 ​ 152 Tassel5
157 ======= 153 =======
158 Tassel5 154
159 ======= 155 -----------
160 ​ 156 Description
161 ----------- 157 -----------
162 Description 158
163 ----------- 159 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
164 ​ 160 | For further informations on tassel, please visit the website_.
165 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. 161
166 | For further informations on tassel, please visit the website_. 162 .. _website: http://www.maizegenetics.net/tassel/
167 ​ 163
168 .. _website: http://www.maizegenetics.net/tassel/ 164 ------------
169 ​ 165 Dependencies
170 ------------ 166 ------------
171 Dependencies 167
172 ------------ 168 Tassel5
173 Tassel5 169
174 tassel_ 5.2.40, Conda version 170 tassel_ 5.2.40, Conda version
175 ​ 171
176 .. _tassel: https://anaconda.org/bioconda/tassel 172 .. _tassel: https://anaconda.org/bioconda/tassel
177 ​ 173
178 ]]></help> 174 ]]></help>
179 <citations> 175 <citations>
180 <citation type="doi">10.1093/bioinformatics/btm308</citation> 176 <citation type="doi">10.1093/bioinformatics/btm308</citation>
181 </citations> 177 </citations>
182 </tool> 178 </tool>