Mercurial > repos > iuc > hyphy_bgm
comparison macros.xml @ 33:5b6b8b08f1a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
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date | Wed, 30 Mar 2022 00:17:25 +0000 |
parents | 12c2453e5040 |
children | 35723f87964d |
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32:12c2453e5040 | 33:5b6b8b08f1a9 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@TOOL_VERSION@">2.5.36</token> | |
3 <xml name="inputs"> | 4 <xml name="inputs"> |
4 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> | 5 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> |
5 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> | 6 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> |
6 </xml> | 7 </xml> |
7 <xml name="bio_tools"> | 8 <xml name="bio_tools"> |
142 <citations> | 143 <citations> |
143 <citation type="doi">10.1093/molbev/msz197</citation> | 144 <citation type="doi">10.1093/molbev/msz197</citation> |
144 <yield/> | 145 <yield/> |
145 </citations> | 146 </citations> |
146 </xml> | 147 </xml> |
147 <token name="@TOOL_VERSION@">2.5.31</token> | |
148 <xml name="requirements"> | 148 <xml name="requirements"> |
149 <requirements> | 149 <requirements> |
150 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> | 150 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> |
151 <yield/> | 151 <yield/> |
152 </requirements> | 152 </requirements> |
154 <xml name="alternative_model_output"> | 154 <xml name="alternative_model_output"> |
155 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json"> | 155 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json"> |
156 <filter>advanced['save_alternative_model']</filter> | 156 <filter>advanced['save_alternative_model']</filter> |
157 </data> | 157 </data> |
158 </xml> | 158 </xml> |
159 <xml name="resample"> | |
160 <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." /> | |
161 </xml> | |
162 <token name="@resample@"><![CDATA[ | |
163 #if $resample: | |
164 --resample $resample | |
165 #end if | |
166 ]]> | |
167 </token> | |
168 | |
159 <token name="@INPUT_TREE@"><![CDATA[ | 169 <token name="@INPUT_TREE@"><![CDATA[ |
160 #if $input_nhx: | 170 #if $input_nhx: |
161 --tree input.nhx | 171 --tree input.nhx |
162 #end if | 172 #end if |
163 ]]> | 173 ]]> |