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comparison ete_species_tree_generator.xml @ 2:03c10736e497 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
author earlhaminst
date Tue, 07 Nov 2017 11:45:13 -0500
parents a4ba317fc713
children 077021c45b96
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1:a4ba317fc713 2:03c10736e497
1 <tool id="ete_species_tree_generator" name="ETE species tree generator" version="3.0.0b35"> 1 <tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@.1">
2 <description>from a list of species using the ETE Toolkit</description> 2 <description>from a list of species using the ETE Toolkit</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="3.0.0b35">ete3</requirement> 4 <import>ete_macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements" />
6 <stdio> 7 <stdio>
7 <!-- Anything other than zero is an error --> 8 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 9 <exit_code range="1:" />
9 </stdio> 10 </stdio>
10 <command> 11 <command>
11 <![CDATA[ 12 <![CDATA[
12 python $__tool_directory__/ete_species_tree_generator.py 13 python '$__tool_directory__/ete_species_tree_generator.py'
13 -s '$speciesFile' 14 -s '$speciesFile'
15 -d $database
16 -o '$outputFile'
14 #if $output_format.treebest == 'yes' 17 #if $output_format.treebest == 'yes'
15 -f 8 18 -f 8
16 #else 19 #else
17 -f ${output_format.format_selector} 20 -f ${output_format.format_selector}
18 #end if 21 #end if
19 -t $output_format.treebest 22 -t $output_format.treebest
20 -d $database
21 ]]> 23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" /> 26 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
27 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
25 <conditional name="output_format"> 28 <conditional name="output_format">
26 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest"> 29 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
27 <option value="yes">Yes</option> 30 <option value="yes">Yes</option>
28 <option value="no" selected="true">No</option> 31 <option value="no" selected="true">No</option>
29 </param> 32 </param>
42 <option value="9">Leaf names (9)</option> 45 <option value="9">Leaf names (9)</option>
43 <option value="100">Topology only (100)</option> 46 <option value="100">Topology only (100)</option>
44 </param> 47 </param>
45 </when> 48 </when>
46 </conditional> 49 </conditional>
47 <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
48 <option value="no" selected="true">No</option>
49 <option value="yes">Yes</option>
50 </param>
51 </inputs> 50 </inputs>
52 <outputs> 51 <outputs>
53 <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/> 52 <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}"/>
54 </outputs> 53 </outputs>
55 <tests> 54 <tests>
56 <test> 55 <test>
57 <param name="speciesFile" ftype="txt" value="species.txt" /> 56 <param name="speciesFile" ftype="txt" value="species.txt" />
57 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
58 <param name="treebest" value="yes" /> 58 <param name="treebest" value="yes" />
59 <output name="outputFile" file="out.nhx" /> 59 <output name="outputFile">
60 <assert_contents>
61 <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />
62 <has_text text=")root;" />
63 </assert_contents>
64 </output>
60 </test> 65 </test>
61 </tests> 66 </tests>
62 <help> 67 <help>
63 <![CDATA[ 68 <![CDATA[
64 Generate a species tree from a list of species using the `ETE Toolkit`_. 69 Generate a species tree from a list of species using the `ETE Toolkit`_.
82 9 leaf names ((D,F),(B,H)); 87 9 leaf names ((D,F),(B,H));
83 100 topology only ((,),(,)); 88 100 topology only ((,),(,));
84 ======= ============================================= ======================================================================================== 89 ======= ============================================= ========================================================================================
85 ]]> 90 ]]>
86 </help> 91 </help>
87 <citations> 92 <expand macro="citations" />
88 <citation type="doi">10.1093/molbev/msw046</citation>
89 </citations>
90 </tool> 93 </tool>