Mercurial > repos > iuc > hyphy_annotate

comparison macros.xml @ 9:88ea681b19d1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Tue, 29 Mar 2022 23:59:39 +0000
parents a016c2cb962d
children d088a1cca4a7
comparison
equal deleted inserted replaced
8:a016c2cb962d 9:88ea681b19d1
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 ]]>