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comparison ete_lineage_generator.xml @ 4:87b6de3ef63e draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 41e40314a9b25a9f3c06a13422d367b68334f593
author earlhaminst
date Thu, 22 Mar 2018 13:25:38 -0400
parents 077021c45b96
children f1eca1158f21
comparison
equal deleted inserted replaced
3:077021c45b96 4:87b6de3ef63e
10 -d '$database' 10 -d '$database'
11 -o '$outputFile' 11 -o '$outputFile'
12 #if $ranks.levels == "full" 12 #if $ranks.levels == "full"
13 -f 13 -f
14 #elif $ranks.levels == "manual" 14 #elif $ranks.levels == "manual"
15 #for $rank in $ranks.manualranks: 15 #for $rank in str($ranks.manualranks).split(','):
16 -r $rank 16 -r $rank
17 #end for 17 #end for
18 #end if 18 #end if
19 #if $compresscond.compress == "-c" 19 #if $compresscond.compress == "-c"
20 $compresscond.compress 20 $compresscond.compress
29 <option value="primary" selected="true">Primary</option> 29 <option value="primary" selected="true">Primary</option>
30 <option value="full">Full</option> 30 <option value="full">Full</option>
31 <option value="manual">Manual</option> 31 <option value="manual">Manual</option>
32 </param> 32 </param>
33 <when value="manual"> 33 <when value="manual">
34 <param name="manualranks" type="select" multiple="true" label="Manual selection of ranks"> 34 <param name="manualranks" type="select" multiple="true" optional="false" label="Manual selection of ranks">
35 <option value="superkingdom">superkingdom</option> 35 <option value="superkingdom">superkingdom</option>
36 <option value="kingdom" selected="true">kingdom</option> 36 <option value="kingdom" selected="true">kingdom</option>
37 <option value="subkingdom">subkingdom</option> 37 <option value="subkingdom">subkingdom</option>
38 <option value="superphylum">superphylum</option> 38 <option value="superphylum">superphylum</option>
39 <option value="phylum" selected="true">phylum</option> 39 <option value="phylum" selected="true">phylum</option>
86 <tests> 86 <tests>
87 <test> 87 <test>
88 <param name="speciesFile" ftype="txt" value="species.txt" /> 88 <param name="speciesFile" ftype="txt" value="species.txt" />
89 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 89 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
90 <param name="compress" value="" /> 90 <param name="compress" value="" />
91 <param name="levels" value="primary" /> 91 <param name="levels" value="full" />
92 <output name="outputFile" file="lineage.txt" /> 92 <output name="outputFile" file="lineage.txt" />
93 </test> 93 </test>
94 <test> 94 <test>
95 <param name="speciesFile" ftype="txt" value="species.txt" /> 95 <param name="speciesFile" ftype="txt" value="species.txt" />
96 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 96 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
108 </test> 108 </test>
109 <test> 109 <test>
110 <param name="speciesFile" ftype="txt" value="species.txt" /> 110 <param name="speciesFile" ftype="txt" value="species.txt" />
111 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 111 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
112 <param name="compress" value="" /> 112 <param name="compress" value="" />
113 <param name="levels" value="full" /> 113 <param name="levels" value="manual" />
114 <param name="manualranks" value="kingdom,family" />
114 <output name="outputFile" file="lineage-full.txt" /> 115 <output name="outputFile" file="lineage-full.txt" />
115 </test> 116 </test>
116 </tests> 117 </tests>
117 <help><![CDATA[ 118 <help><![CDATA[
118 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_. 119 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.