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comparison tassel.xml @ 6:28c0efb3a226 draft

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author dereeper
date Mon, 11 Dec 2023 15:12:25 +0000
parents 652aafd88060
children e2608e112f2a
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5:e94b8b64929c 6:28c0efb3a226
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="5.2.40">tassel</requirement> 4 <requirement type="package" version="5.2.40">tassel</requirement>
5 <requirement type="package" version="1.8">openjdk</requirement>
5 </requirements> 6 </requirements>
6 7 ​
7 <stdio> 8 <stdio>
8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 9 <!-- [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 <exit_code range="1:" level="fatal" />
10 </stdio> 11 </stdio>
11 12 ​
12 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ 13 <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
13 #if $analysis_opts.fonction_selector == "mlm": 14 #if $analysis_opts.fonction_selector == "mlm":
14 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq 15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
15 -fork2 -r $analysis_opts.trait 16 -fork2 -r $analysis_opts.trait
16 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
17 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait 18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
46 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1 47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
47 #else if $analysis_opts.fonction_selector == "ck": 48 #else if $analysis_opts.fonction_selector == "ck":
48 -fork1 -h $hapmap 49 -fork1 -h $hapmap
49 -ck -export tmpdir$$/kinship -runfork1 50 -ck -export tmpdir$$/kinship -runfork1
50 #end if 51 #end if
51 </command> 52 ]]></command>
52 <inputs> 53 <inputs>
53 <param format="txt" name="hapmap" type="data" label="HapMap file"/> 54 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
54 <conditional name="analysis_opts"> 55 <conditional name="analysis_opts">
55 <param name="fonction_selector" type="select" label="Type of analysis"> 56 <param name="fonction_selector" type="select" label="Type of analysis">
56 <option value="mlm" selected="True">MLM</option> 57 <option value="mlm" selected="True">MLM</option>
116 <filter>analysis_opts['fonction_selector'] == "mlm"</filter> 117 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
117 </data> 118 </data>
118 119
119 <data format="txt" name="log" label="Log file"/> 120 <data format="txt" name="log" label="Log file"/>
120 </outputs> 121 </outputs>
121 122 ​
122 <tests> 123 <tests>
123 <test> 124 <test>
124 <param name="hapmap" value="input_hapmap.txt"/> 125 <param name="hapmap" value="input_hapmap.txt"/>
125 <conditional name="analysis_opts"> 126 <conditional name="analysis_opts">
126 <param name="fonction_selector" value="glm"/> 127 <param name="fonction_selector" value="glm"/>
133 <param name="filterAlignMinFreq" value="0.05"/> 134 <param name="filterAlignMinFreq" value="0.05"/>
134 <output name="output1" value="Tassel_output.txt"/> 135 <output name="output1" value="Tassel_output.txt"/>
135 <output name="output2" value="Allele_effects.txt"/> 136 <output name="output2" value="Allele_effects.txt"/>
136 </test> 137 </test>
137 </tests> 138 </tests>
138 139 ​
139 <help><![CDATA[ 140 <help><![CDATA[
140 141 ​
141 142 ​
142 .. class:: infomark 143 .. class:: infomark
143 144 ​
144 **Tassel5** version 5.2.40 145 **Tassel5** version 5.2.40
145 146 ​
146 .. class:: infomark 147 .. class:: infomark
147 148 ​
148 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) 149 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
149 150 ​
150 .. class:: infomark 151 .. class:: infomark
151 152 ​
152 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr 153 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
153 154 ​
154 --------------------------------------------------- 155 ---------------------------------------------------
155 156 ​
156 ======= 157 =======
157 Tassel5 158 Tassel5
158 ======= 159 =======
159 160 ​
160 ----------- 161 -----------
161 Description 162 Description
162 ----------- 163 -----------
163 164 ​
164 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. 165 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
165 | For further informations on tassel, please visit the website_. 166 | For further informations on tassel, please visit the website_.
166 167 ​
167 .. _website: http://www.maizegenetics.net/tassel/ 168 .. _website: http://www.maizegenetics.net/tassel/
168 169 ​
169 ------------ 170 ------------
170 Dependencies 171 Dependencies
171 ------------ 172 ------------
172 Tassel5 173 Tassel5
173 tassel_ 5.2.40, Conda version 174 tassel_ 5.2.40, Conda version
174 175 ​
175 .. _tassel: https://anaconda.org/bioconda/tassel 176 .. _tassel: https://anaconda.org/bioconda/tassel
176 177 ​
177 ]]></help> 178 ]]></help>
178 <citations> 179 <citations>
179 <citation type="doi">10.1093/bioinformatics/btm308</citation> 180 <citation type="doi">10.1093/bioinformatics/btm308</citation>
180 </citations> 181 </citations>
181 </tool> 182 </tool>