Mercurial > repos > earlhaminst > ete

comparison ete_lineage_generator.xml @ 16:e4d5d9a69c9d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:28:17 +0000
parents 1e85af7a29c4
children
comparison
equal deleted inserted replaced
15:1e85af7a29c4 16:e4d5d9a69c9d
1 <tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@"> 1 <tool id="ete_lineage_generator" name="ETE lineage generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>from a list of species/taxids using the ETE Toolkit</description> 2 <description>from a list of species/taxids using the ETE Toolkit</description>
3 <macros> 3 <macros>
4 <import>ete_macros.xml</import> 4 <import>ete_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
86 </outputs> 86 </outputs>
87 <tests> 87 <tests>
88 <test> 88 <test>
89 <param name="speciesFile" ftype="txt" value="species.txt" /> 89 <param name="speciesFile" ftype="txt" value="species.txt" />
90 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 90 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
91 <param name="compress" value="" /> 91 <conditional name="compresscond">
92 <param name="levels" value="full" /> 92 <param name="compress" value="" />
93 </conditional>
94 <conditional name="ranks">
95 <param name="levels" value="full" />
96 </conditional>
93 <output name="outputFile" file="lineage.txt" /> 97 <output name="outputFile" file="lineage.txt" />
94 </test> 98 </test>
95 <test> 99 <test>
96 <param name="speciesFile" ftype="txt" value="species.txt" /> 100 <param name="speciesFile" ftype="txt" value="species.txt" />
97 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 101 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
98 <param name="compress" value="-c" /> 102 <conditional name="compresscond">
99 <param name="levels" value="primary" /> 103 <param name="compress" value="-c" />
104 </conditional>
105 <conditional name="ranks">
106 <param name="levels" value="primary" />
107 </conditional>
100 <output name="outputFile" file="lineage-compress.txt" /> 108 <output name="outputFile" file="lineage-compress.txt" />
101 </test> 109 </test>
102 <test> 110 <test>
103 <param name="speciesFile" ftype="txt" value="species.txt" /> 111 <param name="speciesFile" ftype="txt" value="species.txt" />
104 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 112 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
105 <param name="compress" value="-c" /> 113 <conditional name="compresscond">
106 <param name="levels" value="primary" /> 114 <param name="compress" value="-c" />
107 <param name="lower" value="-l" /> 115 <param name="lower" value="true" />
116 </conditional>
117 <conditional name="ranks">
118 <param name="levels" value="primary" />
119 </conditional>
108 <output name="outputFile" file="lineage-compress-lower.txt" /> 120 <output name="outputFile" file="lineage-compress-lower.txt" />
109 </test> 121 </test>
110 <test> 122 <test>
111 <param name="speciesFile" ftype="txt" value="species.txt" /> 123 <param name="speciesFile" ftype="txt" value="species.txt" />
112 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 124 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
113 <param name="compress" value="" /> 125 <conditional name="compresscond">
114 <param name="levels" value="manual" /> 126 <param name="compress" value="" />
115 <param name="manualranks" value="kingdom,family" /> 127 </conditional>
128 <conditional name="ranks">
129 <param name="levels" value="manual" />
130 <param name="manualranks" value="kingdom,family" />
131 </conditional>
116 <output name="outputFile" file="lineage-full.txt" /> 132 <output name="outputFile" file="lineage-full.txt" />
117 </test> 133 </test>
118 <test> 134 <test>
119 <param name="speciesFile" ftype="txt" value="species.txt" /> 135 <param name="speciesFile" ftype="txt" value="species.txt" />
120 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 136 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
121 <param name="includeid" value="--includeid" /> 137 <param name="includeid" value="true" />
122 <output name="outputFile" file="lineage-wid.txt" /> 138 <output name="outputFile" file="lineage-wid.txt" />
123 </test> 139 </test>
124 <test> 140 <test>
125 <param name="speciesFile" ftype="txt" value="species_ids.txt" /> 141 <param name="speciesFile" ftype="txt" value="species_ids.txt" />
126 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 142 <param name="database" ftype="sqlite" value="taxdump.sqlite" />